Transcriptional control in alicyclobacillus acidocaldarius and associated genes, proteins, and methods

ABSTRACT

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from  Alicyclobacillus acidocaldarius  are provided. Further provided are methods of modulating transcription or transcription or transcriptional control using isolated and/or purified polypeptides and nucleic acid sequences from  Alicyclobacillus acidocaldarius.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.14/256,819, filed Apr. 18, 2014, now U.S. Pat. No. 9,187,753, issuedNov. 17, 2015, which is a divisional of U.S. patent application Ser. No.12/380,008, filed Feb. 20, 2009, now U.S. Pat. No. 8,716,011, issued May6, 2014, which claims the benefit of the filing date of U.S. ProvisionalPatent Application Ser. No. 61/030,820, filed Feb. 22, 2008, for“TRANSCRIPTIONAL CONTROL IN ALICYCLOBACILLUS ACIDOCALDARIUS ANDASSOCIATED GENES, PROTEINS, AND METHODS,” the disclosure of each ofwhich is hereby incorporated herein in its entirety by this reference.

GOVERNMENT RIGHTS

This invention was made with government support under Contract NumberDE-AC07-99ID13727 and Contract Number DE-AC07-05ID14517 awarded by theUnited States Department of Energy. The government has certain rights inthe invention.

(long sequence listing—with parent (Filed with Request to Transfer CRF))

STATEMENT ACCORDING TO 37 C.F.R. §1.821(c) OR (e)-SEQUENCE LISTINGSUBMITTED AS PDF FILE WITH A REQUEST TO TRANSFER CRF FROM PARENTAPPLICATION

Pursuant to 37 C.F.R. §1.821(c) or (e), a file containing a PDF versionof the Sequence Listing has been submitted concomitant with thisapplication, the contents of which are hereby incorporated by reference.The transmittal documents of this application include a Request toTransfer CRF from the parent application.

TECHNICAL FIELD

The present invention relates generally to biotechnology. Morespecifically, the present invention relates to isolated and/or purifiedpolypeptides and nucleic acid sequences encoding polypeptides fromAlicyclobacillus acidocaldarius and methods for their use.

BACKGROUND

Bacterial DNA codes for information that regulates transcription ofgenes into mRNA which codes for proteins or enzymes used for control ofgrowth and processing of energy, carbon and other compounds by the cell.Most of these transcriptional regulators/repressors function to turn onand off genes to minimize expenditure of cellular energy in response totheir growth environment (i.e., presence of growth substrate, metals,temperature, etc.).

BRIEF SUMMARY OF THE INVENTION

Embodiments of the invention relate to purified and/or isolatednucleotide sequences of the genome of Alicyclobacillus acidocaldarius,or a homologue or fragment thereof. In one embodiment of the invention,the nucleotide sequence is selected from at least one of SEQ ID NOS: 2,19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257,274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495,512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733,750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954, 971,988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158, 1175,1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447, 1464,1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651, 1668,1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855, 1872,1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059, 2076,2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263, 2280,2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552, 2569,2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773, 2790,2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and 2928 or ahomologue or fragment thereof. In another embodiment of the invention,the homologue is selected from the group consisting of a nucleotidesequence having at least 80% sequence identity to at least one of SEQ IDNOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240,257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478,495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716,733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954,971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158,1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447,1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651,1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855,1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059,2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263,2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552,2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773,2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and 2928.

Embodiments of the invention may further relate to an isolated and/orpurified nucleic acid sequence comprising a nucleic acid sequenceencoding a polypeptide selected from the group consisting of apolypeptide having at least 90% sequence identity to at least one of SEQID NOS: 1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222,239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460,477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698,715, 732, 749, 766, 783, 800, 817, 834, 851, 868, 885, 902, 819, 936,953, 970, 987, 1004, 1021, 1038, 1055, 1072, 1089, 1106, 1123, 1140,1157, 1174, 1191, 1293, 1310, 1327, 1344, 1361, 1378, 1395, 1412, 1429,1446, 1463, 1480, 1497, 1514, 1531, 1548, 1565, 1582, 1599, 1616, 1633,1650, 1667, 1684, 1701, 1718, 1735, 1752, 1769, 1786, 1803, 1820, 1837,1854, 1871, 1888, 1905, 1922, 1939, 1956, 1973, 1990, 2007, 2024, 2041,2058, 2075, 2092, 2109, 2126, 2143, 2160, 2177, 2194, 2211, 2228, 2245,2262, 2279, 2296, 2313, 2330, 2347, 2364, 2381, 2398, 2415, 2517, 2534,2551, 2568, 2602, 2619, 2636, 2653, 2670, 2687, 2704, 2721, 2738, 2755,2772, 2789, 2806, 2823, 2840, 2859, 2876, 2893, 2910, and 2927.

Embodiments of the invention also relate to isolated and/or purifiedpolypeptides coded for by a nucleotide sequence comprising a nucleotidesequence of the genome of Alicyclobacillus acidocaldarius, or ahomologue or fragment thereof. In one embodiment, the nucleotidesequence comprises a nucleotide sequence selected from the groupconsisting of a nucleotide sequence having at least 80% sequenceidentity to at least one of SEQ ID NOS: 2, 19, 36, 53, 70, 87, 104, 121,138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359,376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597,614, 631, 648, 665, 682, 699, 716, 733, 750, 767, 784, 801, 818, 835,852, 869, 886, 903, 920, 937, 954, 971, 988, 1005, 1022, 1039, 1056,1073, 1090, 1107, 1124, 1141, 1158, 1175, 1192, 1294, 1311, 1328, 1345,1362, 1379, 1396, 1413, 1430, 1447, 1464, 1481, 1498, 1515, 1532, 1549,1566, 1583, 1600, 1617, 1634, 1651, 1668, 1685, 1702, 1719, 1736, 1753,1770, 1787, 1804, 1821, 1838, 1855, 1872, 1889, 1906, 1923, 1940, 1957,1974, 1991, 2008, 2025, 2042, 2059, 2076, 2093, 2110, 2127, 2144, 2161,2178, 2195, 2212, 2229, 2246, 2263, 2280, 2297, 2314, 2331, 2348, 2365,2382, 2399, 2416, 2518, 2535, 2552, 2569, 2603, 2620, 2637, 2654, 2671,2688, 2705, 2722, 2739, 2756, 2773, 2790, 2807, 2824, 2841, 2860, 2877,2894, 2911, and 2928.

In another embodiment of the invention, the nucleotide sequencecomprises a nucleotide sequence selected from at least one of SEQ IDNOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240,257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478,495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716,733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954,971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158,1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447,1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651,1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855,1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059,2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263,2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552,2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773,2790, 2807, 2824, 2841, 2860, 2877, 2894, 2911, and 2928 or a homologueor fragment thereof. In still another embodiment, the polypeptidecomprises an amino acid sequence of SEQ ID NOS: 1, 18, 35, 52, 69, 86,103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324,341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562,579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766, 783, 800,817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021, 1038,1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310, 1327,1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514, 1531,1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718, 1735,1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922, 1939,1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126, 2143,2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330, 2347,2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636, 2653,2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840, 2859,2876, 2893, 2910, and 2927. In yet another embodiment, the polypeptidecomprises an amino acid sequence selected from the group consisting of apolypeptide having at least 90% sequence identity to at least one of SEQID NOS: 1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222,239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460,477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698,715, 732, 749, 766, 783, 800, 817, 834, 851, 868, 885, 902, 819, 936,953, 970, 987, 1004, 1021, 1038, 1055, 1072, 1089, 1106, 1123, 1140,1157, 1174, 1191, 1293, 1310, 1327, 1344, 1361, 1378, 1395, 1412, 1429,1446, 1463, 1480, 1497, 1514, 1531, 1548, 1565, 1582, 1599, 1616, 1633,1650, 1667, 1684, 1701, 1718, 1735, 1752, 1769, 1786, 1803, 1820, 1837,1854, 1871, 1888, 1905, 1922, 1939, 1956, 1973, 1990, 2007, 2024, 2041,2058, 2075, 2092, 2109, 2126, 2143, 2160, 2177, 2194, 2211, 2228, 2245,2262, 2279, 2296, 2313, 2330, 2347, 2364, 2381, 2398, 2415, 2517, 2534,2551, 2568, 2602, 2619, 2636, 2653, 2670, 2687, 2704, 2721, 2738, 2755,2772, 2789, 2806, 2823, 2840, 2859, 2876, 2893, 2910, and 2927.

In embodiments of the invention, the polypeptides may be acidophilicand/or thermophilic. In further embodiments, the polypeptides may beglycosylated, pegylated, and/or otherwise post-translationally modified.

Embodiments of methods include placing a recombinant, purified, and/orisolated polypeptide selected from the group consisting of a polypeptidehaving at least 90% sequence identity to SEQ ID NOS: 1, 18, 35, 52, 69,86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307,324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545,562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766, 783,800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021,1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310,1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514,1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718,1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922,1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126,2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330,2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636,2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840,2859, 2876, 2893, 2910, and 2927 in, or replacing a component, of anin-vitro transcription system such as, by way of non-limiting example, apolymerase chain reaction or a reticulocyte lysatetranscription/translation system.

Further embodiments of methods include placing a cell producing orencoding a recombinant, purified, and/or isolated nucleotide sequencecomprising a nucleotide sequence selected from the group consisting of anucleotide sequences having at least 90% sequence identity to at leastone of the sequences of SEQ ID NOS: 2, 19, 36, 53, 70, 87, 104, 121,138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359,376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597,614, 631, 648, 665, 682, 699, 716, 733, 750, 767, 784, 801, 818, 835,852, 869, 886, 903, 920, 937, 954, 971, 988, 1005, 1022, 1039, 1056,1073, 1090, 1107, 1124, 1141, 1158, 1175, 1192, 1294, 1311, 1328, 1345,1362, 1379, 1396, 1413, 1430, 1447, 1464, 1481, 1498, 1515, 1532, 1549,1566, 1583, 1600, 1617, 1634, 1651, 1668, 1685, 1702, 1719, 1736, 1753,1770, 1787, 1804, 1821, 1838, 1855, 1872, 1889, 1906, 1923, 1940, 1957,1974, 1991, 2008, 2025, 2042, 2059, 2076, 2093, 2110, 2127, 2144, 2161,2178, 2195, 2212, 2229, 2246, 2263, 2280, 2297, 2314, 2331, 2348, 2365,2382, 2399, 2416, 2518, 2535, 2552, 2569, 2603, 2620, 2637, 2654, 2671,2688, 2705, 2722, 2739, 2756, 2773, 2790, 2807, 2824, 2841, 2860, 2877,2894, 2911, and 2928 and/or a recombinant, purified, and/or isolatedpolypeptide selected from the group consisting of a polypeptide havingat least 90% sequence identity to at least one of the sequences of SEQID NOS: 1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222,239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460,477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698,715, 732, 749, 766, 783, 800, 817, 834, 851, 868, 885, 902, 819, 936,953, 970, 987, 1004, 1021, 1038, 1055, 1072, 1089, 1106, 1123, 1140,1157, 1174, 1191, 1293, 1310, 1327, 1344, 1361, 1378, 1395, 1412, 1429,1446, 1463, 1480, 1497, 1514, 1531, 1548, 1565, 1582, 1599, 1616, 1633,1650, 1667, 1684, 1701, 1718, 1735, 1752, 1769, 1786, 1803, 1820, 1837,1854, 1871, 1888, 1905, 1922, 1939, 1956, 1973, 1990, 2007, 2024, 2041,2058, 2075, 2092, 2109, 2126, 2143, 2160, 2177, 2194, 2211, 2228, 2245,2262, 2279, 2296, 2313, 2330, 2347, 2364, 2381, 2398, 2415, 2517, 2534,2551, 2568, 2602, 2619, 2636, 2653, 2670, 2687, 2704, 2721, 2738, 2755,2772, 2789, 2806, 2823, 2840, 2859, 2876, 2893, 2910, and 2927 in anenvironment comprising temperatures at or above about 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/ora pH at, below, and/or above 8, 7, 6, 5, 4, 3, 2, 1, and/or 0.

These and other aspects of the invention will become apparent to theskilled artisan in view of the teachings contained herein.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

FIG. 1 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1446(RAAC01465) and ref|ZP_01666866.1|, ref|YP_001039288.1|,ref|YP_001210812.1|, ref|YP_001111548.1|, and ref|ZP_01576004.1| (SEQ IDNOS: 1448-1452), respectively, which all have the function assigned toSEQ ID NO: 1446 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 2 depicts a sequence alignment (ClustalW) between SEQ ID NO: 443(RAAC00371) and ref|YP_145986.1|, ref|YP_001124263.1|, ref|NP_241028.1|,ref|YP_001210899.1|, and ref|YP_001111617.1| (SEQ ID NOS: 445-449),respectively, which all have the function assigned to SEQ ID NO: 443 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 3A-3C depict a sequence alignment (ClustalW) (ClustalW) betweenSEQ ID NO: 477 (RAAC00408) and ref|ZP_02326346.1|, ref|NP_240992.1|,ref|YP_001124230.1|, ref|YP_145951.1|, and ref|YP_173646.1| (SEQ ID NOS:479-483), respectively, which all have the function assigned to SEQ IDNO: 477 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 4A-4C depict a sequence alignment (ClustalW) (ClustalW) betweenSEQ ID NO: 460 (RAAC00407) and ref|ZP_02326345.1|, ref|YP_001124231.1|,ref|NP_240993.1|, ref|YP_145952.1|, and ref|NP_976431.1| (SEQ ID NOS:462-466), respectively, which all have the function assigned to SEQ IDNO: 460 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 5 depicts a sequence alignment (ClustalW) between SEQ ID NO: 596(RAAC00480) and ref|NP_244660.1|, ref|ZP_01168478.1|,ref|YP_001127419.1|, ref|ZP_01860921.1|, and ref|NP_693930.1| (SEQ IDNOS: 598-602), respectively, which all have the function assigned to SEQID NO: 596 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 6 depicts a sequence alignment (ClustalW) between SEQ ID NO: 307(RAAC00147) and ref|YP_850042.1|, ref|NP_465351.1|, ref|YP_014447.1|,ref|NP_268055.1|, and ref|NP_471274.1| (SEQ ID NOS: 309-313),respectively, which all have the function assigned to SEQ ID NO: 307 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 7 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1752(RAAC01826) and ref|YP_074736.1|, ref|YP_074981.1|, ref|YP_001394390.1|,ref|NP_244228.1|, and ref|YP_001275817.1| (SEQ ID NOS: 1754-1758),respectively, which all have the function assigned to SEQ ID NO: 1752 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 8 depicts a sequence alignment (ClustalW) between SEQ ID NO: 868(RAAC00896) and ref|YP_001126509.1|, ref|YP_148335.1|,ref|ZP_02328521.1|, ref|ZP_01173341.1|, and ref|YP_001376241.1| (SEQ IDNOS: 870-874), respectively, which all have the function assigned to SEQID NO: 868 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 9 depicts a sequence alignment (ClustalW) between SEQ ID NO: 256(RAAC00120) and ref|NP_243422.1|, ref|YP_146980.1|, ref|YP_001125115.1|,ref|ZP_01862300.1|, and ref|ZP_01172495.1| (SEQ ID NOS: 258-262),respectively, which all have the function assigned to SEQ ID NO: 256 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 10 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1956(RAAC02146) and ref|YP_001126333.1|, gb|AAB81194.1|, ref|YP_148161.1|,pdb|1L0O|C, and ref|YP_001487306.1| (SEQ ID NOS: 1958-1962),respectively, which all have the function assigned to SEQ ID NO: 1956 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 11 depicts a sequence alignment (ClustalW) between SEQ ID NO: 273(RAAC00121) and ref|ZP_02330758.1|, ref|YP_001212395.1|,ref|YP_001125116.1|, ref|NP_243420.1|, and ref|ZP_01667054.1| (SEQ IDNOS: 275-279), respectively, which all have the function assigned to SEQID NO: 273 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 12 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2262(RAAC02546) and ref|YP_001512033.1|, ref|NP_976421.1|, ref|NP_842661.1|,ref|NP_829995.1|, and ref|YP_001373458.1| (SEQ ID NOS: 2264-2268),respectively, which all have the function assigned to SEQ ID NO: 2262 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 13 depicts a sequence alignment (ClustalW) between SEQ ID NO: 511(RAAC00418) and ref|YP_077384.1|, ref|YP_001419777.1|, emb|CAA41793.1|,ref|ZP_01173595.1|, and ref|NP_240981.1| (SEQ ID NOS: 513-517),respectively, which all have the function assigned to SEQ ID NO: 511 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 14 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2602(RAAC02968) and ref|YP_001409756.1|, ref|YP_001485343.1|,ref|YP_181606.1|, ref|NP_976421.1|, and ref|NP_842661.1| (SEQ ID NOS:2604-2608), respectively, which all have the function assigned to SEQ IDNO: 2602 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 15 depicts a sequence alignment between SEQ ID NO: 2927 (RAAC03263)and RTHT02135, RTHT02135, RBLH00099, RBSB05130, and RCTH01302 (SEQ IDNOS: 2929-2933), respectively, which all have the function assigned toSEQ ID NO: 2927 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 16 depicts a sequence alignment (ClustalW) between SEQ ID NO: 817(RAAC00856) and ref|YP_001126560.1|, ref|NP_242151.1|, ref|YP_175113.1|,ref|YP_148388.1|, and ref|ZP_01861605.1| (SEQ ID NOS: 819-823),respectively, which all have the function assigned to SEQ ID NO: 817 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 17 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1735(RAAC01814) and ref|YP_148388.1|, ref|YP_001126560.1|, gb|ABY76244.1|,ref|YP_896655.1|, and ref|NP_980714.1| (SEQ ID NOS: 1737-1741),respectively, which all have the function assigned to SEQ ID NO: 1735 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 18 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2381(RAAC02673) and ref|YP_001486125.1|, ref|ZP_01696681.1|,ref|NP_388808.1|, ref|NP_830819.1|, and ref|YP_001643827.1| (SEQ ID NOS:2383-2387), respectively, which all have the function assigned to SEQ IDNO: 2381 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 19 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1905(RAAC02112) and ref|YP_148250.1|, ref|ZP_01725195.1|, ref|NP_390312.1|,ref|ZP_00538565.1|, and ref|YP_001126420.1| (SEQ ID NOS: 1907-1911),respectively, which all have the function assigned to SEQ ID NO: 1905 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 20 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2568(RAAC02902) and ref|YP_147113.1|, ref|NP_243282.1|, ref|YP_001125233.1|,ref|YP_175727.1|, and ref|ZP_02330483.1| (SEQ ID NOS: 2570-2574),respectively, which all have the function assigned to SEQ ID NO: 2568 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 21 depicts a sequence alignment (ClustalW) between SEQ ID NO: 494(RAAC00415) and ref|ZP_01173598.1|, ref|YP_173640.1|, ref|YP_089786.1|,ref|YP_848410.1|, and ref|NP_691027.1| (SEQ ID NOS: 496-500),respectively, which all have the function assigned to SEQ ID NO: 494 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 22A and 22B depict a sequence alignment (ClustalW) between SEQ IDNO: 562 (RAAC00475) and ref|YP_149235.1|, ref|YP_001127411.1|,ref|YP_001377035.1|, gb|AAU09403.1|, and ref|YP_039325.1| (SEQ ID NOS:564-568), respectively, which all have the function assigned to SEQ IDNO: 562 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 23A and 23B depict a sequence alignment (ClustalW) between SEQ IDNO: 2619 (RAAC02984) and ref|ZP_01173129.1|, ref|ZP_01696484.1|,ref|YP_001488275.1|, ref|ZP_02171541.1|, and ref|YP_173520.1| (SEQ IDNOS: 2621-2625), respectively, which all have the function assigned toSEQ ID NO: 2619 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIGS. 24A and 24B depict a sequence alignment (ClustalW) between SEQ IDNO: 2636 (RAAC02994) and ref|NP_244812.1|, ref|ZP_02171541.1|,ref|ZP_01173129.1|, ref|YP_090070.1|, and ref|YP_077660.1| (SEQ ID NOS:2638-2642), respectively, which all have the function assigned to SEQ IDNO: 2636 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 25 depicts a sequence alignment (ClustalW) between SEQ ID NO: 86(RAAC00039) and ref|YP_177603.1|, ref|NP_244925.1|, ref|YP_001423363.1|,ref|ZP_02327875.1|, and ref|ZP_02172038.1| (SEQ ID NOS: 88-92),respectively, which all have the function assigned to SEQ ID NO: 86 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 26 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1871(RAAC02034) and ref|YP_001422137.1|, ref|YP_080133.1|, ref|NP_243941.1|,ref|YP_176156.1|, and ref|YP_001376422.1| (SEQ ID NOS: 1873-1877),respectively, which all have the function assigned to SEQ ID NO: 1871 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 27 depicts a sequence alignment (ClustalW) between SEQ ID NO: 188(RAAC00092) and ref|ZP_01697682.1|, ref|YP_146960.1|, ref|NP_242122.1|,ref|YP_001125095.1|, and ref|ZP_01860230.1| (SEQ ID NOS: 190-194),respectively, which all have the function assigned to SEQ ID NO: 188 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 28 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2143(RAAC02454) and ref|YP_001125095.1|, ref|YP_896293.1|, ref|YP_146960.1|,ref|NP_389392.1|, and ref|ZP_02261942.1| (SEQ ID NOS: 2145-2149),respectively, which all have the function assigned to SEQ ID NO: 2143 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 29 depicts a sequence alignment (ClustalW) between SEQ ID NO: 341(RAAC00212) and ref|YP_752777.1|, ref|YP_001666100.1|, ref|NP_621806.1|,ref|ZP_01666183.1|, and ref|YP_077079.1| (SEQ ID NOS: 343-347),respectively, which all have the function assigned to SEQ ID NO: 341 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 30 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2772(RAAC03236) and ref|YP_001666100.1|, ref|YP_001317994.1|,ref|NP_621806.1|, ref|YP_001181188.1|, and ref|NP_346951.1| (SEQ ID NOS:2774-2778), respectively, which all have the function assigned to SEQ IDNO: 2772 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 31 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2296(RAAC02603) and ref|NP_346951.1|, ref|YP_001181188.1|,ref|YP_001666100.1|, ref|NP_621806.1|, and ref|YP_001317994.1| (SEQ IDNOS: 2298-2302), respectively, which all have the function assigned toSEQ ID NO: 2296 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 32 depicts a sequence alignment (ClustalW) between SEQ ID NO: 324(RAAC00161) and gb|AAC62407.1|, ref|YP_001374031.1|, ref|NP_830661.1|,ref|YP_037204.1|, and ref|NP_979446.1| (SEQ ID NOS: 326-330),respectively, which all have the function assigned to SEQ ID NO: 324 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 33 depicts a sequence alignment (ClustalW) between SEQ ID NO: 919(RAAC00923) and ref|YP_001422239.1|, ref|YP_001420593.1|,ref|ZP_01697004.1|, ref|ZP_01170670.1|, and ref|YP_001486165.1| (SEQ IDNOS: 921-925), respectively, which all have the function assigned to SEQID NO: 919 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 34 depicts a sequence alignment (ClustalW) between SEQ ID NO: 749(RAAC00643) and ref|ZP_02330525.1|, ref|NP_623103.1|,ref|ZP_02330045.1|, ref|YP_001665292.1|, and ref|YP_001665293.1| (SEQ IDNOS: 751-755), respectively, which all have the function assigned to SEQID NO: 749 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 35 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1361(RAAC01427) and ref|NP_240926.1|, ref|ZP_02330558.1|,ref|YP_001419725.1|, ref|NP_829946.1|, and ref|NP_842611.1| (SEQ ID NOS:1363-1367), respectively, which all have the function assigned to SEQ IDNO: 1361 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 36 depicts a sequence alignment (ClustalW) between SEQ ID NO: 426(RAAC00365) and ref|YP_173696.1|, ref|ZP_02329530.1|,ref|ZP_01696660.1|, ref|NP_241105.1|, and ref|YP_001124272.1| (SEQ IDNOS: 428-432), respectively, which all have the function assigned to SEQID NO: 426 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 37A and 37B depict a sequence alignment (ClustalW) between SEQ IDNO: 1531 (RAAC01563) and ref|ZP_01665476.1|, ref|ZP_02259717.1|,ref|YP_036745.1|, ref|YP_028716.1|, and ref|YP_083969.1| (SEQ ID NOS:1533-1537), respectively, which all have the function assigned to SEQ IDNO: 1531 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 38 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2806(RAAC02315) and ref|YP_145847.1|, gb|ABG00342.1|, ref|YP_536482.1|,ref|YP_891181.1|, and ref|YP_799230.1| (SEQ ID NOS: 2808-2812),respectively, which all have the function assigned to SEQ ID NO: 2806 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 39 depicts a sequence alignment (ClustalW) between SEQ ID NO: 103(RAAC00040) and ref|YP_001423364.1|, ref|NP_391977.1|,ref|YP_001488932.1|, ref|YP_093870.1|, and ref|YP_081433.1| (SEQ ID NOS:105-109), respectively, which all have the function assigned to SEQ IDNO: 103 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 40 depicts a sequence alignment (ClustalW) between SEQ ID NO: 205(RAAC00113) and ref|ZP_01697918.1|, ref|YP_001125108.1|,emb|CAJ75583.1|, ref|YP_146973.1|, and ref|ZP_01172488.1| (SEQ ID NOS:207-211), respectively, which all have the function assigned to SEQ IDNO: 205 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 41A and 41B depict a sequence alignment (ClustalW) between SEQ IDNO: 222 (RAAC00117) and ref|ZP_02330014.1|, emb|CAJ75587.1|,ref|YP_146977.1|, ref|YP_001125112.1|, and ref|NP_243425.1| (SEQ ID NOS:224-228), respectively, which all have the function assigned to SEQ IDNO: 222 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 42 depicts a sequence alignment (ClustalW) between SEQ ID NO: 239(RAAC00118) and ref|YP_078922.1|, ref|YP_001375784.1|,ref|ZP_02171874.1|, ref|YP_001646530.1|, and gb|AAN04557.1| (SEQ ID NOS:241-245), respectively, which all have the function assigned to SEQ IDNO: 239 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 43 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1344(RAAC01377) and ref|YP_147952.1|, ref|YP_520670.1|, ref|YP_001395809.1|,ref|YP_001309701.1|, and ref|YP_001643660.1| (SEQ ID NOS: 1346-1350),respectively, which all have the function assigned to SEQ ID NO: 1344 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 44A and 44B depict a sequence alignment (ClustalW) between SEQ IDNO: 2840 (RAAC02381) and ref|NP_622177.1|, ref|YP_848858.1|,ref|YP_001374688.1|, ref|NP_470039.1|, and ref|ZP_01929325.1| (SEQ IDNOS: 2842-2846), respectively, which all have the function assigned toSEQ ID NO: 2840 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 45 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1038(RAAC00991) and ref|ZP_02327412.1|, ref|YP_001487207.1|,ref|ZP_01172765.1|, ref|NP_831314.1|, and ref|NP_844008.1| (SEQ ID NOS:1040-1044), respectively, which all have the function assigned to SEQ IDNO: 1038 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 46 depicts a sequence alignment (ClustalW) between SEQ ID NO: 766(RAAC00650) and ref|YP_001127183.1|, ref|ZP_02038504.1|,ref|YP_001647987.1|, ref|YP_001377114.1|, and ref|NP_835081.1| (SEQ IDNOS: 768-772), respectively, which all have the function assigned to SEQID NO: 766 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 47 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2041(RAAC02421) and ref|ZP_01721811.1|, ref|NP_241897.1|,ref|YP_001486101.1|, ref|ZP_01170532.1|, and ref|ZP_02327994.1| (SEQ IDNOS: 2043-2047), respectively, which all have the function assigned toSEQ ID NO: 2041 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIGS. 48A and 48B depict a sequence alignment (ClustalW) between SEQ IDNO: 1922 (RAAC02142) and ref|ZP_01860158.1|, ref|YP_148164.1|,ref|NP_242401.1|, ref|YP_001126336.1|, and ref|YP_001421751.1| (SEQ IDNOS: 1924-1928), respectively, which all have the function assigned toSEQ ID NO: 1922 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIGS. 49A and 49B depict a sequence alignment (ClustalW) between SEQ IDNO: 2687 (RAAC03015) and ref|NP_628606.1|, ref|ZP_02061285.1|,ref|NP_824958.1|, emb|CAA04971.1|, and gb|AAC32488.1| (SEQ ID NOS:2689-2693), respectively, which all have the function assigned to SEQ IDNO: 2687 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 50A and 50B depict a sequence alignment (ClustalW) between SEQ IDNO: 2517 (RAAC02227) and ref|YP_430213.1|, ref|YP_001212426.1|,ref|YP_001663198.1|, ref|YP_360920.1|, and ref|YP_001665129.1| (SEQ IDNOS: 2519-2523), respectively, which all have the function assigned toSEQ ID NO: 2517 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 51 depicts a sequence alignment (ClustalW) between SEQ ID NO: 834(RAAC00872) and ref|NP_622598.1|, ref|YP_001320854.1|,ref|YP_001665389.1|, ref|YP_001037463.1|, and ref|YP_001512768.1| (SEQID NOS: 836-840), respectively, which all have the function assigned toSEQ ID NO: 834 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 52 depicts a sequence alignment (ClustalW) between SEQ ID NO: 120(RAAC00045) and ref|ZP_02172045.1|, ref|ZP_01189194.1|,ref|NP_244931.1|, ref|YP_001213468.1|, and ref|YP_358877.1| (SEQ ID NOS:122-126), respectively, which all have the function assigned to SEQ IDNO: 120 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 53A and 53B depict a sequence alignment (ClustalW) between SEQ IDNO: 2092 (RAAC02428) and dbj|BAB83769.1|, ref|YP_146913.1|,sp|P11961|ODP2_BACST, ref|ZP_01696305.1|, and ref|YP_001125047.1| (SEQID NOS: 2094-2098), respectively, which all have the function assignedto SEQ ID NO: 2092 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIGS. 54A and 54B depict a sequence alignment (ClustalW) between SEQ IDNO: 1650 (RAAC01659) and ref|ZP_02326222.1|, ref|NP_241081.1|,ref|YP_074242.1|, ref|YP_001153408.1|, and ref|NP_560158.1| (SEQ ID NOS:1652-1656), respectively, which all have the function assigned to SEQ IDNO: 1650 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 55 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1701(RAAC01745) and ref|YP_001127228.1|, ref|YP_149070.1|,ref|ZP_00539127.1|, ref|ZP_02326224.1|, and ref|NP_241079.1| (SEQ IDNOS: 1703-1707), respectively, which all have the function assigned toSEQ ID NO: 1701 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 56 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1718(RAAC01746) and ref|YP_149069.1|, ref|YP_001127227.1|,ref|ZP_00539126.1|, ref|YP_001125046.1|, and ref|NP_833691.1| (SEQ IDNOS: 1720-1724), respectively, which all have the function assigned toSEQ ID NO: 1718 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 57 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2058(RAAC02426) and ref|NP_243521.1|, pdb|1W85|A, sp|P21873|ODPA_BACST,ref|YP_001421036.1|, and ref|YP_146911.1| (SEQ ID NOS: 2060-2064),respectively, which all have the function assigned to SEQ ID NO: 2058 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 58 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2075(RAAC02427) and ref|ZP_01696304.1|, sp|P21874|ODPB_BACST,ref|YP_001125046.1|, pdb|1W85|B, and ref|YP_146912.1| (SEQ ID NOS:2077-2081), respectively, which all have the function assigned to SEQ IDNO: 2075 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 59 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1616(RAAC01657) and ref|ZP_02326224.1|, dbj|BAB40585.1|, ref|NP_241079.1|,ref|YP_001126012.1|, and ref|ZP_01171269.1| (SEQ ID NOS: 1618-1622),respectively, which all have the function assigned to SEQ ID NO: 1616 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 60 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1633(RAAC01658) and ref|ZP_02326223.1|, ref|NP_241080.1|, dbj|BAB40586.1|,ref|YP_001126011.1|, and ref|NP_693798.1| (SEQ ID NOS: 1635-1639),respectively, which all have the function assigned to SEQ ID NO: 1633 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 61A and 61B depict a sequence alignment (ClustalW) between SEQ IDNO: 630 (RAAC00484) and ref|YP_001125466.1|, ref|ZP_01697095.1|,ref|YP_147353.1|, ref|ZP_01886631.1|, and ref|YP_077737.1| (SEQ ID NOS:632-636), respectively, which all have the function assigned to SEQ IDNO: 630 Table 1. Amino acids conserved among all sequences are indictedby a “*” and generally conserved amino acids are indicated by a “:”.

FIG. 62 depicts a sequence alignment (ClustalW) between SEQ ID NO: 613(RAAC00483) and ref|NP_886151.1|, ref|YP_147354.1|, ref|YP_001125467.1|,ref|YP_001420062.1|, and ref|NP_242684.1| (SEQ ID NOS: 615-619),respectively, which all have the function assigned to SEQ ID NO: 613 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 63 depicts a sequence alignment (ClustalW) between SEQ ID NO: 290(RAAC00134) and ref|ZP_01860800.1|, ref|YP_147000.1|,ref|ZP_01695960.1|, ref|YP_001125127.1|, and ref|YP_806677.1| (SEQ IDNOS: 292-296), respectively, which all have the function assigned to SEQID NO: 290 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 64 depicts a sequence alignment (ClustalW) between SEQ ID NO: 358(RAAC00215) and ref|YP_145879.1|, ref|ZP_01697513.1|,ref|YP_001124157.1|, ref|ZP_01174007.1|, and ref|YP_001642924.1| (SEQ IDNOS: 360-364), respectively, which all have the function assigned to SEQID NO: 358 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 65 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2177(RAAC02164) and ref|YP_359129.1|, ref|ZP_02127016.1|,ref|YP_001540277.1|, pdb|1M2N|A, and pdb|1M2K|A (SEQ ID NOS: 2179-2183),respectively, which all have the function assigned to SEQ ID NO: 2177 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 66A-66C depict a sequence alignment (ClustalW) between SEQ ID NO:1395 (RAAC01438) and ref|YP_173587.1|, ref|NP_240935.1|,ref|YP_001373418.1|, ref|YP_892975.1|, and ref|NP_976379.1| (SEQ ID NOS:1397-1401), respectively, which all have the function assigned to SEQ IDNO: 1395 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 67 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2755(RAAC03184) and ref|YP_001105447.1|, ref|YP_117520.1|, ref|YP_046943.1|,ref|YP_707186.1|, and ref|YP_001337847.1| (SEQ ID NOS: 2757-2761),respectively, which all have the function assigned to SEQ ID NO: 2755 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 68 depicts a sequence alignment between SEQ ID NO: 2859 (RAAC02740)and ref|NP_391246.1|, ref|YP_001488252.1|, ref|NP_244416.1|,ref|YP_001112264.1|, and ref|YP_430670.1| (SEQ ID NOS: 2861-2865),respectively, which all have the function assigned to SEQ ID NO: 2859 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 69 depicts a sequence alignment between SEQ ID NO: 2893 (RAAC02937)and ref|YP_075413.1|, ref|YP_001662816.1|, ref|YP_001664674.1|,ref|YP_827514.1|, and ref|YP_827514.1| (SEQ ID NOS: 2895-2899),respectively, which all have the function assigned to SEQ ID NO: 2893 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 70 depicts a sequence alignment (ClustalW) between SEQ ID NO: 783(RAAC00675) and ref|YP_001373772.1|, ref|YP_034761.1|, ref|YP_893335.1|,ref|ZP_00237972.1|, and ref|ZP_02329595.1| (SEQ ID NOS: 785-789),respectively, which all have the function assigned to SEQ ID NO: 783 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 71 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2789(RAAC02292) and gb|AAB91591.1|, ref|YP_001422657.1|, ref|NP_391247.1|,ref|YP_093160.1|, and ref|NP_391246.1| (SEQ ID NOS: 2791-2795),respectively, which all have the function assigned to SEQ ID NO: 2789 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 72 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1599(RAAC01655) and ref|ZP_00235680.1|, ref|NP_241278.1|, ref|NP_845841.1|,ref|ZP_02260616.1|, and ref|ZP_02256143.1| (SEQ ID NOS: 1601-1605),respectively, which all have the function assigned to SEQ ID NO: 1599Table 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 73 depicts a sequence alignment (ClustalW) between SEQ ID NO: 545(RAAC00436) and ref|ZP_02171828.1|, ref|YP_077369.1|,ref|YP_001485328.1|, ref|ZP_02329455.1|, and ref|YP_001419762.1| (SEQ IDNOS: 547-551), respectively, which all have the function assigned to SEQID NO: 545 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 74 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1429(RAAC01464) and ref|YP_001485324.1|, ref|YP_001124204.1|,ref|YP_145925.1|, ref|YP_077366.1|, and ref|NP_829977.1| (SEQ ID NOS:1431-1435), respectively, which all have the function assigned to SEQ IDNO: 1429 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 75 depicts a sequence alignment (ClustalW) between SEQ ID NO: 698(RAAC00579) and ref|ZP_01440002.1|, ref|NP_896891.1|,ref|YP_001623237.1|, ref|ZP_01419169.1|, and ref|ZP_01084741.1| (SEQ IDNOS: 700-704), respectively, which all have the function assigned to SEQID NO: 698 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 76 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2721(RAAC03156) and ref|YP_954024.1|, ref|YP_001360254.1|,ref|YP_001156989.1|, ref|ZP_00050136.21, and ref|YP_591607.1| (SEQ IDNOS: 2723-2727), respectively, which all have the function assigned toSEQ ID NO: 2721 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 77 depicts a sequence alignment (ClustalW) between SEQ ID NO: 715(RAAC00603) and ref|YP_001309477.1|, ref|YP_001180339.1|,ref|NP_242735.1|, ref|YP_173905.1|, and ref|ZP_00603386.1| (SEQ ID NOS:717-721), respectively, which all have the function assigned to SEQ IDNO: 715 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 78 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2738(RAAC03180) and ref|YP_001664041.1|, ref|YP_001210714.1|,ref|NP_242309.1|, ref|ZP_02038515.1|, and ref|YP_085042.1| (SEQ ID NOS:2740-2744), respectively, which all have the function assigned to SEQ IDNO: 2738 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 79 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2024(RAAC02417) and ref|NP_469419.1|, ref|ZP_02309926.1|,ref|ZP_01926077.1|, ref|ZP_01941236.1|, and ref|YP_001111866.1| (SEQ IDNOS: 2026-2030), respectively, which all have the function assigned toSEQ ID NO: 2024 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 80 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1786(RAAC01912) and ref|YP_001103030.1|, ref|YP_001363698.1|,ref|NP_625321.1|, ref|NP_822608.1|, and ref|ZP_00996757.1| (SEQ ID NOS:1788-1792), respectively, which all have the function assigned to SEQ IDNO: 1786 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 81 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2330(RAAC02663) and ref|YP_527240.1|, ref|NP_435364.1|, ref|YP_001313948.1|,ref|YP_001169444.1|, and ref|ZP_01509063.1| (SEQ ID NOS: 2332-2336),respectively, which all have the function assigned to SEQ ID NO: 2330 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 82 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1191(RAAC01158) and ref|YP_077724.1|, ref|YP_643029.1|, ref|YP_174340.1|,ref|YP_001308645.1|, and ref|YP_516602.1| (SEQ ID NOS: 1193-1197),respectively, which all have the function assigned to SEQ ID NO: 1191 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 83 depicts a sequence alignment (ClustalW) between SEQ ID NO: 137(RAAC00068) and ref|ZP_02328287.1|, ref|YP_001420528.1|,ref|YP_430032.1|, ref|ZP_02082978.1|, and ref|ZP_01962813.1| (SEQ IDNOS: 139-143), respectively, which all have the function assigned to SEQID NO: 137 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 84 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1055(RAAC01035) and ref|YP_642998.1|, ref|NP_822795.1|, emb|CAJ88752.1|,ref|YP_001191149.1|, and ref|YP_752794.1| (SEQ ID NOS: 1057-1061),respectively, which all have the function assigned to SEQ ID NO: 1055 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 85 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1854(RAAC02031) and ref|YP_148128.1|, ref|YP_001126297.1|, ref|YP_900875.1|,ref|ZP_01662088.1|, and ref|ZP_01697892.1| (SEQ ID NOS: 1856-1860),respectively, which all have the function assigned to SEQ ID NO: 1854 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 86 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2653(RAAC03005) and ref|YP_001127075.1|, ref|YP_148880.1|, ref|YP_832996.1|,ref|YP_949591.1|, and ref|YP_950253.1| (SEQ ID NOS: 2655-2659),respectively, which all have the function assigned to SEQ ID NO: 2653 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 87 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2160(RAAC02459) and ref|YP_073926.1|, emb|CAB08003.1|, ref|YP_431134.1|,ref|YP_001422711.1|, and ref|YP_080763.1| (SEQ ID NOS: 2162-2166),respectively, which all have the function assigned to SEQ ID NO: 2160 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 88 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1293(RAAC01353) and RAAC01353_nuc, ref|YP_147389.1|, ref|NP_243003.1|,ref|YP_001125502.1|, and ref|YP_001665938.1| (SEQ ID NOS: 1294-1298),respectively, which all have the function assigned to SEQ ID NO: 1293 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 89 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2109(RAAC02432) and ref|ZP_02329176.1|, ref|YP_076367.1|, ref|NP_694155.1|,ref|YP_001126042.1|, and ref|YP_643152.1| (SEQ ID NOS: 2111-2115),respectively, which all have the function assigned to SEQ ID NO: 2109 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 90 depicts a sequence alignment (ClustalW) between SEQ ID NO: 681(RAAC00570) and emb|CAB65654.1|, ref|YP_001662226.1|,ref|YP_001664166.1|, ref|NP_624096.1|, and ref|ZP_02171282.1| (SEQ IDNOS: 683-687), respectively, which all have the function assigned to SEQID NO: 681 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 91 depicts a sequence alignment (ClustalW) between SEQ ID NO: 375(RAAC00269) and ref|ZP_01188890.1|, ref|ZP_01188246.1|,ref|ZP_01188241.1|, ref|NP_242794.1|, and ref|NP_244559.1| (SEQ ID NOS:377-381), respectively, which all have the function assigned to SEQ IDNO: 375 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 92 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1837(RAAC02012) and ref|YP_430255.1|, ref|YP_518526.1|, ref|ZP_01369294.1|,ref|YP_361384.1|, and ref|YP_001213325.1| (SEQ ID NOS: 1839-1843),respectively, which all have the function assigned to SEQ ID NO: 1837 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 93 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1667(RAAC01701) and ref|NP_691275.1|, ref|NP_354021.1|, ref|YP_174284.1|,ref|ZP_01074644.1|, and ref|NP_772010.1| (SEQ ID NOS: 1669-1673),respectively, which all have the function assigned to SEQ ID NO: 1667 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 94 depicts a sequence alignment (ClustalW) between SEQ ID NO: 936(RAAC00927) and ref|ZP_02330514.1|, ref|NP_347485.1|,ref|YP_001253394.1|, ref|YP_001308605.1|, and ref|YP_001376921.1| (SEQID NOS: 938-942), respectively, which all have the function assigned toSEQ ID NO: 936 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 95 depicts a sequence alignment (ClustalW) between SEQ ID NO: 953(RAAC00935) and ref|YP_001422559.1|, ref|NP_391166.1|, gb|AAB87745.1|,pdb|1S3J|A, and ref|YP_001643469.1| (SEQ ID NOS: 955-959), respectively,which all have the function assigned to SEQ ID NO: 953 in Table 1. Aminoacids conserved among all sequences are indicted by a “*” and generallyconserved amino acids are indicated by a “:”.

FIG. 96 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1888(RAAC02041) and ref|NP_693030.1|, ref|YP_001320949.1|,ref|YP_001512727.1|, ref|YP_001126687.1|, and ref|YP_148522.1| (SEQ IDNOS: 1890-1894), respectively, which all have the function assigned toSEQ ID NO: 1888 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 97 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2670(RAAC02241) and ref|NP_629113.1|, ref|NP_824479.1|, ref|YP_001508494.1|,ref|ZP_01169478.1|, and ref|NP_631123.1| (SEQ ID NOS: 2672-2676),respectively, which all have the function assigned to SEQ ID NO: 2670 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 98 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2347(RAAC02671) and ref|NP_388620.1|, ref|YP_001420380.1|, ref|YP_090401.1|,ref|YP_077997.1|, and ref|YP_714968.1| (SEQ ID NOS: 2349-2353),respectively, which all have the function assigned to SEQ ID NO: 2347 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 99 depicts a sequence alignment (ClustalW) between SEQ ID NO: 664(RAAC00549) and ref|YP_427081.1|, ref|YP_001141973.1|, ref|YP_927240.1|,ref|YP_001141729.1|, and ref|YP_856665.1| (SEQ ID NOS: 666-670),respectively, which all have the function assigned to SEQ ID NO: 664 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 100 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1123(RAAC01080) and dbj|BAA00729.1|, ref|NP_389627.1|, ref|ZP_02328256.1|,ref|NP_833433.1|, and ref|YP_001375615.1| (SEQ ID NOS: 1125-1129),respectively, which all have the function assigned to SEQ ID NO: 1123 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 101 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1140(RAAC01126) and ref|YP_146517.1|, ref|ZP_00739458.1|,ref|YP_001124699.1|, ref|YP_893832.1|, and ref|NP_830863.1| (SEQ ID NOS:1142-1146), respectively, which all have the function assigned to SEQ IDNO: 664 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 102 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1174(RAAC01138) and ref|NP_832103.1|, ref|YP_894956.1|, ref|ZP_02215257.1|,ref|NP_978750.1|, and ref|NP_844783.1| (SEQ ID NOS: 1176-1180),respectively, which all have the function assigned to SEQ ID NO: 1174 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 103 depicts a sequence alignment (ClustalW) between SEQ ID NO: 409(RAAC00354) and ref|YP_001309939.1|, ref|YP_001643723.1|,ref|YP_079403.1|, ref|YP_001647188.1|, and ref|NP_980994.1| (SEQ ID NOS:411-415), respectively, which all have the function assigned to SEQ IDNO: 409 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 104 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2415(RAAC02712) and ref|YP_036650.1|, ref|NP_978853.1|, ref|ZP_01173627.1|,ref|NP_844911.1|, and ref|ZP_02256518.1| (SEQ ID NOS: 2417-2421),respectively, which all have the function assigned to SEQ ID NO: 2415 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 105 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1072(RAAC01059) and ref|ZP_02327699.1|, ref|YP_001126706.1|,ref|YP_148542.1|, ref|NP_243968.1|, and ref|YP_360433.1| (SEQ ID NOS:1074-1078), respectively, which all have the function assigned to SEQ IDNO: 1072 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 106 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1565(RAAC01638) and ref|YP_076316.1|, ref|YP_603589.1|, ref|NP_296097.1|,ref|YP_004584.1|, and ref|YP_144239.1| (SEQ ID NOS: 1567-1571),respectively, which all have the function assigned to SEQ ID NO: 1565 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 107 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1973(RAAC02161) and ref|YP_148132.1|, ref|YP_001126301.1|,ref|ZP_02330236.1|, ref|NP_242446.1|, and ref|YP_175331.1| (SEQ ID NOS:1975-1979), respectively, which all have the function assigned to SEQ IDNO: 1973 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 108 depicts a sequence alignment (ClustalW) between SEQ ID NO: 392(RAAC00349) and ref|YP_430046.1|, ref|YP_358986.1|, ref|YP_001213400.1|,ref|ZP_02330078.1|, and ref|YP_001114520.1| (SEQ ID NOS: 394-398),respectively, which all have the function assigned to SEQ ID NO: 392 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 109 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1327(RAAC01375) and ref|YP_079987.1|, ref|YP_001634921.1|, ref|YP_290510.1|,ref|YP_001423330.1|, and ref|YP_001422015.1| (SEQ ID NOS: 1329-1333),respectively, which all have the function assigned to SEQ ID NO: 1327 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 110 depicts a sequence alignment (ClustalW) between SEQ ID NO: 18(RAAC00013) and ref|YP_146744.1|, ref|YP_001647744.1|, ref|NP_981573.1|,ref|ZP_02255842.1|, and ref|YP_897365.1| (SEQ ID NOS: 20-24),respectively, which all have the function assigned to SEQ ID NO: 18 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 111 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1480(RAAC01493) and ref|YP_075596.1|, ref|YP_430668.1|, ref|YP_590553.1|,ref|YP_478499.1|, and ref|YP_001668480.1| (SEQ ID NOS: 1482-1486),respectively, which all have the function assigned to SEQ ID NO: 1480 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 112 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1582(RAAC01653) and ref|ZP_00743391.1|, ref|YP_001375561.1|,ref|YP_896056.1|, ref|NP_845992.1|, and ref|ZP_02254866.1| (SEQ ID NOS:1584-1588), respectively, which all have the function assigned to SEQ IDNO: 1582 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 113 depicts a sequence alignment (ClustalW) between SEQ ID NO: 528(RAAC00430) and ref|YP_001210836.1|, ref|YP_001111557.1|,ref|YP_001485333.1|, ref|NP_240971.1|, and ref|NP_387969.1| (SEQ ID NOS:530-534), respectively, which all have the function assigned to SEQ IDNO: 528 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 114 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2823(RAAC02359) and ref|NP_832076.1|, ref|YP_001645033.1|, ref|NP_844759.1|,ref|YP_001375058.1|, and ref|YP_535778.1| (SEQ ID NOS: 2825-2829),respectively, which all have the function assigned to SEQ ID NO: 2823 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 115 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2279(RAAC02589) and ref|ZP_00591928.1|, ref|YP_001003150.1|,ref|NP_046614.1|, ref|YP_375842.1|, and ref|YP_001131112.1| (SEQ ID NOS:2281-2285), respectively, which all have the function assigned to SEQ IDNO: 2279 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 116 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1412(RAAC01442) and ref|ZP_02170919.1|, ref|YP_535778.1|,ref|ZP_01862118.1|, ref|NP_692713.1|, and ref|YP_359077.1| (SEQ ID NOS:1414-1418), respectively, which all have the function assigned to SEQ IDNO: 1412 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 117 depicts a sequence alignment (ClustalW) between SEQ ID NO: 69(RAAC00027) and ref|YP_001213441.1|, ref|NP_244917.1|,ref|YP_001377189.1|, ref|YP_149334.1|, and ref|YP_077145.1| (SEQ ID NOS:71-75), respectively, which all have the function assigned to SEQ ID NO:69 in Table 1. Amino acids conserved among all sequences are indicted bya “*” and generally conserved amino acids are indicated by a “:”.

FIG. 118 depicts a sequence alignment (ClustalW) between SEQ ID NO: 2245(RAAC02508) and ref|NP_624000.1|, ref|YP_001662406.1|,ref|YP_001664279.1|, ref|YP_001038261.1|, and ref|YP_001394883.1| (SEQID NOS: 2247-2251), respectively, which all have the function assignedto SEQ ID NO: 2245 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 119 depicts a sequence alignment (ClustalW) between SEQ ID NO: 885(RAAC00905) and ref|ZP_00739566.1|, ref|NP_830389.1|,ref|YP_001643379.1|, ref|ZP_00237866.1|, and ref|YP_034830.1| (SEQ IDNOS: 887-891), respectively, which all have the function assigned to SEQID NO: 885 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 120 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1769(RAAC01903) and ref|YP_001244333.1|, emb|CAI44346.1|,ref|ZP_02128221.1|, ref|NP_228001.1|, and ref|ZP_02171167.1| (SEQ IDNOS: 1771-1775), respectively, which all have the function assigned toSEQ ID NO: 1769 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 121 depicts a sequence alignment (ClustalW) between SEQ ID NO: 987(RAAC00981) and ref|YP_290547.1|, ref|YP_074752.1|, ref|YP_480150.1|,ref|YP_001509772.1|, and ref|NP_627230.1| (SEQ ID NOS: 989-993),respectively, which all have the function assigned to SEQ ID NO: 987 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 122A and 122B depict a sequence alignment (ClustalW) between SEQID NO: 1004 (RAAC00986) and ref|YP_001489923.1|, ref|ZP_01964315.1|,ref|NP_937072.1|, ref|NP_762428.1|, and ref|ZP_01847462.1| (SEQ ID NOS:1006-1010), respectively, which all have the function assigned to SEQ IDNO: 1004 Table 1. Amino acids conserved among all sequences are indictedby a “*” and generally conserved amino acids are indicated by a “:”.

FIGS. 123A and 123B depict a sequence alignment (ClustalW) between SEQID NO: 2704 (RAAC03031) and ref|ZP_01170738.1|, ref|ZP_00539543.1|,ref|ZP_02168828.1|, ref|ZP_01856429.1|, and ref|YP_001114416.1| (SEQ IDNOS: 2706-2710), respectively, which all have the function assigned toSEQ ID NO: 2704 Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 124 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1803(RAAC01956) and pdb|1B4A|A, sp|O31408|ARGR_BACST, ref|ZP_00538558.1|,ref|NP_243643.1|, and ref|YP_001126414.1| (SEQ ID NOS: 1805-1809),respectively, which all have the function assigned to SEQ ID NO: 1803 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 125 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1497(RAAC01498) and ref|YP_001127098.1|, ref|YP_148912.1|,ref|ZP_01696601.1|, ref|YP_176517.1|, and ref|ZP_01171675.1| (SEQ IDNOS: 1499-1503), respectively, which all have the function assigned toSEQ ID NO: 1497 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 126 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1548(RAAC01624) and ref|YP_090740.1|, ref|YP_078338.1|, ref|NP_243093.1|,ref|YP_001126180.1|, and ref|YP_001422307.1| (SEQ ID NOS: 1550-1554),respectively, which all have the function assigned to SEQ ID NO: 1548 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 127 depicts a sequence alignment (ClustalW) between SEQ ID NO: 171(RAAC00077) and ref|ZP_01696173.1|, ref|ZP_02327860.1|,ref|ZP_00539488.1|, ref|NP_694112.1|, and ref|YP_034511.1| (SEQ ID NOS:173-177), respectively, which all have the function assigned to SEQ IDNO: 171 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 128 depicts a sequence alignment (ClustalW) between SEQ ID NO: 851(RAAC00876) and ref|ZP_02170056.1|, ref|YP_079889.1|, ref|NP_980690.1|,ref|ZP_02257686.1|, and ref|YP_038371.1| (SEQ ID NOS: 853-857),respectively, which all have the function assigned to SEQ ID NO: 851 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 129 depicts a sequence alignment (ClustalW) between SEQ ID NO: 647(RAAC00525) and ref|YP_001488458.1|, ref|ZP_01665756.1|,ref|NP_347033.1|, ref|YP_080909.1|, and ref|YP_841318.1| (SEQ ID NOS:649-653), respectively, which all have the function assigned to SEQ IDNO: 647 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 130 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1089(RAAC01072) and ref|YP_849514.1|, ref|ZP_02320157.1|, ref|YP_013918.1|,ref|ZP_02330749.1|, and ref|NP_470676.1| (SEQ ID NOS: 1091-1095),respectively, which all have the function assigned to SEQ ID NO: 1089 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 131 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1310(RAAC01366) and ref|YP_849898.1|, ref|NP_471127.1|, ref|NP_465208.1|,ref|YP_001124617.1|, and ref|YP_146331.1| (SEQ ID NOS: 1312-1316),respectively, which all have the function assigned to SEQ ID NO: 1310Table 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 132 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1378(RAAC01431) and ref|ZP_01666690.1|, ref|YP_077070.1|,ref|ZP_01173986.1|, ref|YP_814057.1|, and ref|NP_964223.1| (SEQ ID NOS:1380-1384), respectively, which all have the function assigned to SEQ IDNO: 1378 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 133 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1514(RAAC01505) and ref|YP_149084.1|, ref|YP_001127265.1|, ref|YP_074599.1|,ref|YP_001661816.1|, and ref|NP_621898.1| (SEQ ID NOS: 1516-1520),respectively, which all have the function assigned to SEQ ID NO: 1514 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 134 depicts a sequence alignment (ClustalW) between SEQ ID NO: 1514(RAAC01505) and ref|YP_149084.1|, ref|YP_001127265.1|, ref|YP_074599.1|,ref|YP_001661816.1|, and ref|NP_621898.1| (SEQ ID NOS: 1516-1520),respectively, which all have the function assigned to SEQ ID NO: 1514 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 135 depicts a sequence alignment between SEQ ID NO: 1820(RAAC01972) and ref|ZP_01171531.1|, ref|YP_001391734.1|,ref|YP_001308325.1|, ref|YP_518781.1|, and ref|YP_001254935.1| (SEQ IDNOS: 1822-1826), respectively, which all have the function assigned toSEQ ID NO: 1820 Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 136 depicts a sequence alignment between SEQ ID NO: 154 (RAAC00076)and ref|YP_001488917.1|, ref|YP_079193.1|, ref|NP_241876.1|,ref|YP_174035.1|, and ref|ZP_01169176.1| (SEQ ID NOS: 156-160),respectively, which all have the function assigned to SEQ ID NO: 154 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 137 depicts a sequence alignment between SEQ ID NO: 1939(RAAC02144) and ref|ZP_02327651.1|, sp|O32720|SP2AA_PAEPO,ref|NP_833792.1|, ref|NP_846529.1|, and ref|YP_001646701.1| (SEQ ID NOS:1941-1945), respectively, which all have the function assigned to SEQ IDNO: 1939 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 138A and 138B depict a sequence alignment between SEQ ID NO: 2126(RAAC02439) and ref|YP_001125957.1|, ref|YP_147806.1|,ref|ZP_01695872.1|, ref|NP_693661.1|, and ref|ZP_01666100.1| (SEQ IDNOS: 2128-2132), respectively, which all have the function assigned toSEQ ID NO: 2126 Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 139 depicts a sequence alignment between SEQ ID NO: 970 (RAAC00944)and ref|YP_001488778.1|, ref|YP_174256.1|, ref|YP_081277.1|,ref|YP_711801.1|, and ref|YP_804091.1| (SEQ ID NOS: 972-976),respectively, which all have the function assigned to SEQ ID NO: 970 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 140A and 140B depict a sequence alignment between SEQ ID NO: 2313(RAAC02632) and ref|ZP_01695369.1|, ref|NP_764957.1|, ref|NP_646484.1|,ref|YP_001332652.1|, and ref|NP_372249.1| (SEQ ID NOS: 2315-2319),respectively, which all have the function assigned to SEQ ID NO: 2313 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 141 depicts a sequence alignment between SEQ ID NO: 2211(RAAC02474) and ref|ZP_02329050.1|, ref|YP_148935.1|, gb|AAX09759.1|,ref|YP_001127122.1|, and ref|YP_001376898.1| (SEQ ID NOS: 2213-2217),respectively, which all have the function assigned to SEQ ID NO: 2211 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 142 depicts a sequence alignment between SEQ ID NO: 732 (RAAC00625)and ref|NP_244107.1|, ref|ZP_01188060.1|, ref|YP_176259.1|,ref|YP_148663.1|, and ref|YP_001126805.1| (SEQ ID NOS: 734-738),respectively, which all have the function assigned to SEQ ID NO: 732 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 143 depicts a sequence alignment between SEQ ID NO: 800 (RAAC00733)and ref|ZP_01697803.1|, ref|YP_001488326.1|, ref|ZP_01860336.1|,ref|NP_834817.1|, and ref|NP_693386.1| (SEQ ID NOS: 802-806),respectively, which all have the function assigned to SEQ ID NO: 800 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 144 depicts a sequence alignment between SEQ ID NO: 2194(RAAC02466) and ref|ZP_01860336.1|, ref|ZP_02327791.1|,ref|NP_244433.1|, ref|ZP_01171669.1|, and ref|YP_001488326.1| (SEQ IDNOS: 2196-2200), respectively, which all have the function assigned toSEQ ID NO: 2194 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 145 depicts a sequence alignment between SEQ ID NO: 2398(RAAC02678) and ref|YP_001124914.1|, ref|YP_146760.1|,ref|YP_001319371.1|, ref|ZP_01723416.1|, and ref|ZP_00742387.1| (SEQ IDNOS: 2400-2404), respectively, which all have the function assigned toSEQ ID NO: 2398 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 146 depicts a sequence alignment between SEQ ID NO: 2228(RAAC02507) and ref|YP_517080.1|, ref|ZP_02185068.1|,ref|YP_001394884.1|, ref|ZP_01574787.1|, and ref|YP_001559227.1| (SEQ IDNOS: 2230-2234), respectively, which all have the function assigned toSEQ ID NO: 2228 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIGS. 147A and 147B depict a sequence alignment between SEQ ID NO: 902(RAAC00906) and ref|ZP_01667455.1|, ref|ZP_01515931.1|,ref|YP_001430381.1|, ref|YP_001637100.1|, and ref|YP_146183.1| (SEQ IDNOS: 904-908), respectively, which all have the function assigned to SEQID NO: 902 Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 148 depicts a sequence alignment between SEQ ID NO: 2364(RAAC02211) and ref|YP_005108.1|, ref|YP_144769.1|, ref|YP_001124914.1|,ref|YP_001157480.1|, and ref|ZP_01773683.1| (SEQ ID NOS: 2366-2370),respectively, which all have the function assigned to SEQ ID NO: 2364 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 149A and 149B depict a sequence alignment between SEQ ID NO: 1463(RAAC01489) and ref|ZP_01696335.1|, ref|ZP_01667455.1|,ref|ZP_00739567.1|, ref|YP_001037228.1|, and ref|NP_830390.1| (SEQ IDNOS: 1465-1469), respectively, which all have the function assigned toSEQ ID NO: 1463 Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 150A and 150B depict a sequence alignment between SEQ ID NO: 2007(RAAC02391) and ref|ZP_01697157.1|, ref|YP_001212380.1|,ref|ZP_00539202.1|, ref|NP_693085.1|, and ref|ZP_02329946.1| (SEQ IDNOS: 2009-2013), respectively, which all have the function assigned toSEQ ID NO: 2007 Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 151A and 151B depict a sequence alignment between SEQ ID NO: 2551(RAAC02885) and ref|YP_147095.1|, ref|ZP_01171502.1|,ref|YP_001125215.1|, ref|YP_001486785.1|, and ref|ZP_01861001.1| (SEQ IDNOS: 2553-2557), respectively, which all have the function assigned toSEQ ID NO: 2551 Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIG. 152 depicts a sequence alignment between SEQ ID NO: 2534(RAAC02876) and ref|YP_001125206.1|, ref|ZP_01696550.1|,ref|YP_001410204.1|, ref|ZP_01860990.1|, and ref|NP_243310.1| (SEQ IDNOS: 2536-2540), respectively, which all have the function assigned toSEQ ID NO: 2534 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

FIG. 153 depicts a sequence alignment between SEQ ID NO: 1021(RAAC00987) and ref|YP_001559801.1|, ref|ZP_01696550.1|,ref|YP_753552.1|, ref|NP_243310.1|, and ref|ZP_01725653.1| (SEQ ID NOS:1023-1027), respectively, which all have the function assigned to SEQ IDNO: 1021 in Table 1. Amino acids conserved among all sequences areindicted by a “*” and generally conserved amino acids are indicated by a“:”.

FIGS. 154A and 154B depict a sequence alignment between SEQ ID NO: 1990(RAAC02162) and ref|YP_148131.1|, ref|YP_001126300.1|, ref|YP_079616.1|,ref|NP_390192.1|, and ref|YP_001487274.1| (SEQ ID NOS: 1992-1996),respectively, which all have the function assigned to SEQ ID NO: 1990Table 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 155 depicts a sequence alignment between SEQ ID NO: 1 (RAAC00012)and ref|YP_907563.1|, ref|YP_955166.1|, ref|ZP_00997175.1|,ref|YP_001133548.1|, and ref|YP_829143.1| (SEQ ID NOS: 3-7),respectively, which all have the function assigned to SEQ ID NO: 1 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 156A and 156B depict a sequence alignment between SEQ ID NO: 2876(RAAC02761) and emb|CAG29823.1|, ref|NP_923516.1|, ref|ZP_02329377.1|,gb|EAY57526.1|, and ref|YP_149098.1| (SEQ ID NOS: 2878-2882),respectively, which all have the function assigned to SEQ ID NO: 2876 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 157 depicts a sequence alignment between SEQ ID NO: 579 (RAAC00477)and ref|YP_001377039.1|, ref|NP_244654.1|, ref|YP_001647908.1|,ref|YP_897521.1|, and ref|ZP_00744427.1| (SEQ ID NOS: 581-585),respectively, which all have the function assigned to SEQ ID NO: 579 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 158A and 158B depict a sequence alignment between SEQ ID NO: 35(RAAC00019) and ref|ZP_02169265.1|, ref|YP_848463.1|, ref|NP_694373.1|,ref|ZP_01695448.1|, and ref|ZP_00539458.1| (SEQ ID NOS: 37-41),respectively, which all have the function assigned to SEQ ID NO: 35 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIG. 159 depicts a sequence alignment between SEQ ID NO: 52 (RAAC00020)and ref|ZP_01169692.1|, ref|ZP_01695449.1|, ref|YP_001127497.1|,ref|YP_149327.1|, and ref|YP_534941.1| (SEQ ID NOS: 54-58),respectively, which all have the function assigned to SEQ ID NO: 52 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 160A and 160B depict a sequence alignment between SEQ ID NO: 1684(RAAC01715) and gb|EDQ48509.1|, gb|EDQ48476.1|, ref|ZP_01575425.1|,ref|ZP_02025790.1|, and ref|YP_001662047.1| (SEQ ID NOS: 1686-1690),respectively, which all have the function assigned to SEQ ID NO: 1684 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 161A-161C depict a sequence alignment between SEQ ID NO: 1157(RAAC01137) and ref|NP_978751.1|, ref|ZP_00741477.1|, ref|YP_894957.1|,ref|NP_844784.1|, and ref|ZP_02259481.1| (SEQ ID NOS: 1159-1163),respectively, which all have the function assigned to SEQ ID NO: 1157 inTable 1. Amino acids conserved among all sequences are indicted by a “*”and generally conserved amino acids are indicated by a “:”.

FIGS. 162A-162C depict a sequence alignment between SEQ ID NO: 2910(RAAC03013) and ref|ZP_02168855.1|, ref|NP_470526.1|,ref|ZP_02320069.1|, ref|ZP_01927122.1|, and ref|YP_013834.1| (SEQ IDNOS: 2912-2916), respectively, which all have the function assigned toSEQ ID NO: 2910 in Table 1. Amino acids conserved among all sequencesare indicted by a “*” and generally conserved amino acids are indicatedby a “:”.

DETAILED DESCRIPTION OF THE INVENTION

Bacterial DNA codes for information that regulates transcription ofgenes into mRNA, which codes for proteins or enzymes used for; controlof growth, and processing of energy, carbon and other compounds by thecell. Most of these transcriptional regulators/repressors function toturn on and off genes to minimize expenditure of cellular energy inresponse to their growth environment (i.e., presence of growthsubstrate, metals, temperature, etc.). This can become a problem relatedto process development because regulation and control of enzymes for aspecific reaction may lead to suboptimal growth or suboptimal productionof a desired metabolite (enzyme or compound). The genome ofAlicyclobacillus acidocaldarius strain ATCC 27009 contains numerouscoding sequences for transcriptional regulators and repressors ofproteins related to growth, and processing of carbon by the cell. Theseregulators and repressors may directly affect expression of glycosylhydrolase and/or esterase enzymes for processing of biomass outside thecell, as well as controlling production of valuable secondarymetabolites.

Metabolic engineering through modification (genetic engineering) ofthese regulatory responses for transcription is one approach foroptimization of cellular processes, by way of non-limiting example,Alicyclobacillus acidocaldarius. Control of these genes will allow forover-expression of desired pathways (e.g., production of glycosylhydrolases, organic acids or alcohols), or likewise elimination orcausing reduced expression of genes leading to undesired pathways orproducts (e.g., proteins that control transcription of glycosylhydrolase genes). Control of these genes, or using them as loci forcontrolling/optimizing carbon processing in organisms, such as, by wayof non-limiting example, the thermoacidophile Alicyclobacillusacidocaldarius has not been previously attempted using genes andproteins from Alicyclobacillus acidocaldarius; thereby, making use oftranscriptional regulators from this source novel.

Embodiments of the invention include genes and associated proteinsrelated to regulation of growth and metabolism of the thermoacidophileAlicyclobacillus acidocaldarius. Coding sequences for genes related tothese processes were determined from sequence information generated fromsequencing the genome of Alicyclobacillus acidocaldarius. These genesand proteins may represent targets for metabolic engineering ofAlicyclobacillus acidocaldarius or other organisms. Non-limitingexamples of nucleotide sequences found within the genome ofAlicyclobacillus acidocaldarius, and amino acids coded thereby,associated with regulation of growth and carbon metabolism are listed inTable 1. Regulators and repressors may be, without limitation, of thefollowing classes: regulators that control growth, including celldivision and growth under aerobic and anaerobic conditions; regulatorsthat respond to environmental conditions such as temperature, metalconcentration and metabolite concentration; regulators of secondarymetabolite pathways such as amino acids, organic acids, alcohols,antibiotics, antibiotic resistance, enzymes related to DNA processingand others; repressors related to carbon processing operons that respondto the presence or absence of organic compounds in the growthenvironment; signal transduction regulators that control phases ofgrowth and carbon processing; regulators that control the response ofAlicyclobacillus acidocaldarius to its growth environment allowingmovement toward carbon sources or biofilm formation on a carbon source;and others.

Embodiments of the invention relate in part to the gene sequences and/orprotein sequences comprising genes and/or proteins of Alicyclobacillusacidocaldarius. Genes and proteins included are those which play a rolein transcription and transcriptional control. Intracellular enzymeactivities may be thermophilic and/or acidophilic in nature and generalexamples of similar genes are described in the literature. Classes ofgenes, sequences, enzymes and factors include, but are not limited to,those listed in Table 1.

TABLE 1 Alicyclobacillus acidocaldarius genes related to transcriptionand transcriptional regulation Reference Gene Sequence Protein SequenceFunction RAAC00012 SEQ ID NO: 2 SEQ ID NO: 1 C4-dicarboxylate transportprotein RAAC00013 SEQ ID NO: 19 SEQ ID NO: 18 Transcriptionalregulators, LysR family RAAC00019 SEQ ID NO: 36 SEQ ID NO: 35Two-component sensor kinase yycG RAAC00020 SEQ ID NO: 53 SEQ ID NO: 52Two-component response regulator yycF RAAC00027 SEQ ID NO: 70 SEQ ID NO:69 Single-strand DNA binding protein RAAC00039 SEQ ID NO: 87 SEQ ID NO:86 Stage 0 sporulation protein J RAAC00040 SEQ ID NO: 104 SEQ ID NO: 103Chromosome partitioning protein parA RAAC00045 SEQ ID NO: 121 SEQ ID NO:120 Jag protein RAAC00068 SEQ ID NO: 138 SEQ ID NO: 137 Transcriptionalregulator, GntR family RAAC00076 SEQ ID NO: 155 SEQ ID NO: 154 Trprepressor binding protein RAAC00077 SEQ ID NO: 172 SEQ ID NO: 171Gluconate operon transcriptional repressor RAAC00092 SEQ ID NO: 189 SEQID NO: 188 Prespore specific transcriptional activator rsfA RAAC00113SEQ ID NO: 206 SEQ ID NO: 205 Cell-division initiation protein DivIBRAAC00117 SEQ ID NO: 223 SEQ ID NO: 222 Cell division protein ftsARAAC00118 SEQ ID NO: 240 SEQ ID NO: 239 Cell division protein ftsZRAAC00120 SEQ ID NO: 257 SEQ ID NO: 256 RNA polymerase sigma-E factorRAAC00121 SEQ ID NO: 274 SEQ ID NO: 273 RNA polymerase sigma-G factorRAAC00134 SEQ ID NO: 291 SEQ ID NO: 290 Pyrimidine operon regulatoryprotein pyrR RAAC00147 SEQ ID NO: 308 SEQ ID NO: 307 DNA-directed RNApolymerase omega chain RAAC00161 SEQ ID NO: 325 SEQ ID NO: 324 Smallacid-soluble spore protein RAAC00212 SEQ ID NO: 342 SEQ ID NO: 341Transcription state regulatory protein abrB RAAC00215 SEQ ID NO: 359 SEQID NO: 358 Phosphorelay inhibitor RAAC00269 SEQ ID NO: 376 SEQ ID NO:375 Transcriptional regulator, LacI family RAAC00349 SEQ ID NO: 393 SEQID NO: 392 Transcriptional regulator, AsnC family RAAC00354 SEQ ID NO:410 SEQ ID NO: 409 Transcriptional regulator, TetR family RAAC00365 SEQID NO: 427 SEQ ID NO: 426 N-acetylmuramoyl-L-alanine amidase RAAC00371SEQ ID NO: 444 SEQ ID NO: 443 DNA-directed RNA polymerase alpha chainRAAC00407 SEQ ID NO: 461 SEQ ID NO: 460 DNA-directed RNA polymerasebeta' chain RAAC00408 SEQ ID NO: 478 SEQ ID NO: 477 DNA-directed RNApolymerase beta chain RAAC00415 SEQ ID NO: 495 SEQ ID NO: 494Transcription antitermination protein nusG RAAC00418 SEQ ID NO: 512 SEQID NO: 511 RNA polymerase sigma-H factor RAAC00430 SEQ ID NO: 529 SEQ IDNO: 528 DNA-binding protein RAAC00436 SEQ ID NO: 546 SEQ ID NO: 545Transcriptional regulator ctsR RAAC00475 SEQ ID NO: 563 SEQ ID NO: 562Transcription termination factor rho RAAC00477 SEQ ID NO: 580 SEQ ID NO:579 Sporulation initiation phosphotransferase F RAAC00480 SEQ ID NO: 597SEQ ID NO: 596 DNA-directed RNA polymerase delta chain RAAC00483 SEQ IDNO: 614 SEQ ID NO: 613 Regulator of kinase autophosphorylation inhibitorRAAC00484 SEQ ID NO: 631 SEQ ID NO: 630 Kinase autophosphorylationinhibitor kipI RAAC00525 SEQ ID NO: 648 SEQ ID NO: 647 Kdg operonrepressor RAAC00549 SEQ ID NO: 665 SEQ ID NO: 664 Transcriptionalregulator, MerR family RAAC00570 SEQ ID NO: 682 SEQ ID NO: 681Transcriptional regulator, LacI family RAAC00579 SEQ ID NO: 699 SEQ IDNO: 698 Transcriptional regulator, ArsR family RAAC00603 SEQ ID NO: 716SEQ ID NO: 715 Transcriptional regulator, ArsR family RAAC00625 SEQ IDNO: 733 SEQ ID NO: 732 Catabolite control protein A RAAC00643 SEQ ID NO:750 SEQ ID NO: 749 Small acid-soluble spore protein RAAC00650 SEQ ID NO:767 SEQ ID NO: 766 Glycosyltransferase RAAC00675 SEQ ID NO: 784 SEQ IDNO: 783 Transcriptional regulator RAAC00733 SEQ ID NO: 801 SEQ ID NO:800 Catabolite repression protein crh RAAC00856 SEQ ID NO: 818 SEQ IDNO: 817 RNA polymerase sigma-K factor RAAC00872 SEQ ID NO: 835 SEQ IDNO: 834 Spore protease RAAC00876 SEQ ID NO: 852 SEQ ID NO: 851Heat-inducible transcription repressor hrcA RAAC00896 SEQ ID NO: 869 SEQID NO: 868 RNA polymerase sigma factor rpoD RAAC00905 SEQ ID NO: 886 SEQID NO: 885 Two-component response regulator RAAC00906 SEQ ID NO: 903 SEQID NO: 902 Two component system histidine kinase RAAC00923 SEQ ID NO:920 SEQ ID NO: 919 Small acid-soluble spore protein RAAC00927 SEQ ID NO:937 SEQ ID NO: 936 Transcriptional regulator, MarR family RAAC00935 SEQID NO: 954 SEQ ID NO: 953 Transcriptional regulator, MarR familyRAAC00944 SEQ ID NO: 971 SEQ ID NO: 970 Transcriptional activator tenARAAC00981 SEQ ID NO: 988 SEQ ID NO: 987 Two-component response regulatorRAAC00986 SEQ ID NO: 1005 SEQ ID NO: 1004 Two-component responseregulator RAAC00987 SEQ ID NO: 1022 SEQ ID NO: 1021 Chemotaxis proteincheY RAAC00991 SEQ ID NO: 1039 SEQ ID NO: 1038 GlycosyltransferaseRAAC01035 SEQ ID NO: 1056 SEQ ID NO: 1055 Transcriptional regulator,GntR family RAAC01059 SEQ ID NO: 1073 SEQ ID NO: 1072 Transcriptionalregulator, TetR family RAAC01072 SEQ ID NO: 1090 SEQ ID NO: 1089Repressor LexA RAAC01078 SEQ ID NO: 1107 SEQ ID NO: 1106 Ribose operonrepressor RAAC01080 SEQ ID NO: 1124 SEQ ID NO: 1123 Transcriptionalregulator, MerR family RAAC01126 SEQ ID NO: 1141 SEQ ID NO: 1140Transcriptional regulator, TetR family RAAC01137 SEQ ID NO: 1158 SEQ IDNO: 1157 Transporter, MMPL family RAAC01138 SEQ ID NO: 1175 SEQ ID NO:1174 Transcriptional regulator, TetR family RAAC01158 SEQ ID NO: 1192SEQ ID NO: 1191 Transcriptional regulator, GntR family RAAC01353 SEQ IDNO: 1294 SEQ ID NO: 1293 Transcriptional regulator, IclR familyRAAC01366 SEQ ID NO: 1311 SEQ ID NO: 1310 Peroxide operon regulatorRAAC01375 SEQ ID NO: 1328 SEQ ID NO: 1327 Transcriptional regulators,LysR family RAAC01377 SEQ ID NO: 1345 SEQ ID NO: 1344Glycosyltransferase RAAC01427 SEQ ID NO: 1362 SEQ ID NO: 1361 SspFprotein RAAC01431 SEQ ID NO: 1379 SEQ ID NO: 1378 Pur operon repressorRAAC01438 SEQ ID NO: 1396 SEQ ID NO: 1395 Transcription-repair couplingfactor RAAC01442 SEQ ID NO: 1413 SEQ ID NO: 1412 DNA-binding protein HURAAC01464 SEQ ID NO: 1430 SEQ ID NO: 1429 Transcriptional regulator, Xrefamily RAAC01465 SEQ ID NO: 1447 SEQ ID NO: 1446 Transcriptionelongation factor greA RAAC01489 SEQ ID NO: 1464 SEQ ID NO: 1463 Twocomponent system histidine kinase RAAC01493 SEQ ID NO: 1481 SEQ ID NO:1480 Transcriptional regulators, LysR family RAAC01498 SEQ ID NO: 1498SEQ ID NO: 1497 Central glycolytic genes regulator RAAC01505 SEQ ID NO:1515 SEQ ID NO: 1514 Ribose operon repressor RAAC01563 SEQ ID NO: 1532SEQ ID NO: 1531 Sporulation kinase D RAAC01624 SEQ ID NO: 1549 SEQ IDNO: 1548 Ebg operon repressor RAAC01638 SEQ ID NO: 1566 SEQ ID NO: 1565Transcriptional regulator, TetR family RAAC01653 SEQ ID NO: 1583 SEQ IDNO: 1582 Transcriptional regulators, LysR family RAAC01655 SEQ ID NO:1600 SEQ ID NO: 1599 Transcriptional regulator RAAC01657 SEQ ID NO: 1617SEQ ID NO: 1616 Pyruvate dehydrogenase (acetyl- transferring) RAAC01658SEQ ID NO: 1634 SEQ ID NO: 1633 Pyruvate dehydrogenase (acetyl-transferring) RAAC01659 SEQ ID NO: 1651 SEQ ID NO: 1650Dihydrolipoyllysine-residue acetyltransferase RAAC01701 SEQ ID NO: 1668SEQ ID NO: 1667 Transcriptional regulator, MarR family RAAC01715 SEQ IDNO: 1685 SEQ ID NO: 1684 Two-component response regulator yesN RAAC01745SEQ ID NO: 1702 SEQ ID NO: 1701 Pyruvate dehydrogenase (acetyl-transferring) RAAC01746 SEQ ID NO: 1719 SEQ ID NO: 1718 Pyruvatedehydrogenase (acetyl- transferring) RAAC01814 SEQ ID NO: 1736 SEQ IDNO: 1735 RNA polymerase sigma-K factor RAAC01826 SEQ ID NO: 1753 SEQ IDNO: 1752 RNA polymerase ECF-type sigma factor RAAC01903 SEQ ID NO: 1770SEQ ID NO: 1769 Two-component response regulator RAAC01912 SEQ ID NO:1787 SEQ ID NO: 1786 Transcriptional regulator, DeoR family RAAC01956SEQ ID NO: 1804 SEQ ID NO: 1803 Arginine repressor, argR RAAC01972 SEQID NO: 1821 SEQ ID NO: 1820 Transcription pleiotropic repressor codYRAAC02012 SEQ ID NO: 1838 SEQ ID NO: 1837 Transcriptional regulator,LytR family RAAC02031 SEQ ID NO: 1855 SEQ ID NO: 1854 Transcriptionalregulator, GntR family RAAC02034 SEQ ID NO: 1872 SEQ ID NO: 1871Germination protein gerE RAAC02041 SEQ ID NO: 1889 SEQ ID NO: 1888Transcriptional regulator, MarR family RAAC02112 SEQ ID NO: 1906 SEQ IDNO: 1905 N utilization substance protein B RAAC02142 SEQ ID NO: 1923 SEQID NO: 1922 Serine-type D-Ala-D-Ala carboxypeptidase RAAC02144 SEQ IDNO: 1940 SEQ ID NO: 1939 Anti-sigma F factor antagonist RAAC02146 SEQ IDNO: 1957 SEQ ID NO: 1956 RNA polymerase sigma-F factor RAAC02161 SEQ IDNO: 1974 SEQ ID NO: 1973 Transcriptional regulatory protein resDRAAC02162 SEQ ID NO: 1991 SEQ ID NO: 1990 Sensor protein resE RAAC02391SEQ ID NO: 2008 SEQ ID NO: 2007 Phosphate regulon sensor protein phoRRAAC02417 SEQ ID NO: 2025 SEQ ID NO: 2024 Transcriptional regulator,Cro/CI family RAAC02421 SEQ ID NO: 2042 SEQ ID NO: 2041Glycosyltransferase RAAC02426 SEQ ID NO: 2059 SEQ ID NO: 2058 Pyruvatedehydrogenase (acetyl- transferring) RAAC02427 SEQ ID NO: 2076 SEQ IDNO: 2075 Pyruvate dehydrogenase (acetyl- transferring) RAAC02428 SEQ IDNO: 2093 SEQ ID NO: 2092 Dihydrolipoyllysine-residue acetyltransferaseRAAC02432 SEQ ID NO: 2110 SEQ ID NO: 2109 Transcriptional regulator,IclR family RAAC02439 SEQ ID NO: 2127 SEQ ID NO: 2126 Sigma-54-dependenttranscriptional activator RAAC02454 SEQ ID NO: 2144 SEQ ID NO: 2143Prespore specific transcriptional activator rsfA RAAC02459 SEQ ID NO:2161 SEQ ID NO: 2160 Transcriptional regulator, GntR family RAAC02164SEQ ID NO: 2178 SEQ ID NO: 2177 SIR2 family protein RAAC02466 SEQ ID NO:2195 SEQ ID NO: 2194 Catabolite repression protein crh RAAC02474 SEQ IDNO: 2212 SEQ ID NO: 2211 Hpr(ser) Kinase/Phosphatase RAAC02507 SEQ IDNO: 2229 SEQ ID NO: 2228 Two component system histidine kinase RAAC02508SEQ ID NO: 2246 SEQ ID NO: 2245 Two-component response regulatorRAAC02546 SEQ ID NO: 2263 SEQ ID NO: 2262 RNA polymerase sigma-H factorRAAC02589 SEQ ID NO: 2280 SEQ ID NO: 2279 DNA-binding protein HURAAC02603 SEQ ID NO: 2297 SEQ ID NO: 2296 Transcription state regulatoryprotein abrB RAAC02632 SEQ ID NO: 2314 SEQ ID NO: 2313 Hpr(ser)Kinase/Phosphatase RAAC02663 SEQ ID NO: 2331 SEQ ID NO: 2330Transcriptional regulator, GntR family RAAC02671 SEQ ID NO: 2348 SEQ IDNO: 2347 Transcriptional regulator, MerR family RAAC02211 SEQ ID NO:2365 SEQ ID NO: 2364 Two component system histidine kinase RAAC02673 SEQID NO: 2382 SEQ ID NO: 2381 Glycerol uptake operon antiterminatorregulatory protein RAAC02678 SEQ ID NO: 2399 SEQ ID NO: 2398 Twocomponent system histidine kinase RAAC02712 SEQ ID NO: 2416 SEQ ID NO:2415 Transcriptional regulator, TetR family RAAC02227 SEQ ID NO: 2518SEQ ID NO: 2517 Serine-type D-Ala-D-Ala carboxypeptidase RAAC02876 SEQID NO: 2535 SEQ ID NO: 2534 Chemotaxis protein cheY RAAC02885 SEQ ID NO:2552 SEQ ID NO: 2551 Chemotaxis protein cheA RAAC02902 SEQ ID NO: 2569SEQ ID NO: 2568 N utilization substance protein A RAAC02968 SEQ ID NO:2603 SEQ ID NO: 2602 RNA polymerase sigma-H factor RAAC02984 SEQ ID NO:2620 SEQ ID NO: 2619 Arginine utilization regulatory protein rocRRAAC02994 SEQ ID NO: 2637 SEQ ID NO: 2636 Arginine utilizationregulatory protein rocR RAAC03005 SEQ ID NO: 2654 SEQ ID NO: 2653Transcriptional regulator, GntR family RAAC02241 SEQ ID NO: 2671 SEQ IDNO: 2670 Transcriptional regulator, MarR family RAAC03015 SEQ ID NO:2688 SEQ ID NO: 2687 Serine-type D-Ala-D-Ala carboxypeptidase RAAC03031SEQ ID NO: 2705 SEQ ID NO: 2704 Two-component response regulatorRAAC03156 SEQ ID NO: 2722 SEQ ID NO: 2721 Transcriptional regulator,ArsR family RAAC03180 SEQ ID NO: 2739 SEQ ID NO: 2738 Transcriptionalregulator, Cro/CI family RAAC03184 SEQ ID NO: 2756 SEQ ID NO: 2755Transcriptional regulator RAAC03236 SEQ ID NO: 2773 SEQ ID NO: 2772Transcription state regulatory protein abrB RAAC02292 SEQ ID NO: 2790SEQ ID NO: 2789 Transcriptional regulator RAAC02315 SEQ ID NO: 2807 SEQID NO: 2806 Chromosome partitioning protein parA RAAC02359 SEQ ID NO:2824 SEQ ID NO: 2823 DNA-binding protein HU RAAC02381 SEQ ID NO: 2841SEQ ID NO: 2840 Glycosyltransferase SEQ ID NO: 2857Catabolite-responsive element SEQ ID NO: 2858 Catabolite responsiveelement RAAC02740 SEQ ID NO: 2860 SEQ ID NO: 2859 Transcriptionalregulator RAAC02761 SEQ ID NO: 2877 SEQ ID NO: 2876 Sensor protein kdpDRAAC02937 SEQ ID NO: 2894 SEQ ID NO: 2893 Transcriptional regulatorRAAC03013 SEQ ID NO: 2911 SEQ ID NO: 2910 Transporter, MMPL familyRAAC03263 SEQ ID NO: 2928 SEQ ID NO: 2927 RNA polymerase sigma-H factor

The present invention relates to nucleotides sequences comprisingisolated and/or purified nucleotide sequences of the genome ofAlicyclobacillus acidocaldarius selected from the sequences of SEQ IDNOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240,257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478,495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716,733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954,971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158,1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447,1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651,1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855,1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059,2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263,2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552,2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773,2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and 2928 orone of their fragments.

The present invention likewise relates to isolated and/or purifiednucleotide sequences, characterized in that they comprise at least oneof: a) a nucleotide sequence of at least one of the sequences of SEQ IDNOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240,257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478,495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716,733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954,971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158,1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447,1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651,1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855,1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059,2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263,2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552,2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773,2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and 2928 orone of their fragments; b) a nucleotide sequence homologous to anucleotide sequence such as defined in a); c) a nucleotide sequencecomplementary to a nucleotide sequence such as defined in a) or b), anda nucleotide sequence of their corresponding RNA; d) a nucleotidesequence capable of hybridizing under stringent conditions with asequence such as defined in a), b) or c); e) a nucleotide sequencecomprising a sequence such as defined in a), b), c) or d); and f) anucleotide sequence modified by a nucleotide sequence such as defined ina), b), c), d) or e).

Nucleotide, polynucleotide, or nucleic acid sequence will be understoodaccording to the present invention as meaning both a double-stranded orsingle-stranded DNA in the monomeric and dimeric (so-called in tandem)forms and the transcription products of the DNAs.

Aspects of the invention relate to nucleotide sequences in which it hasbeen possible to isolate, purify or partially purify, starting fromseparation methods such as, for example, ion-exchange chromatography, byexclusion based on molecular size, or by affinity, or, alternatively,fractionation techniques based on solubility in different solvents, orstarting from methods of genetic engineering such as amplification,cloning, and subcloning, it being possible for the sequences of theinvention to be carried by vectors.

Isolated and/or purified nucleotide sequence fragment according to theinvention will be understood as designating any nucleotide fragment ofthe genome of Alicyclobacillus acidocaldarius, and may include, by wayof non-limiting example, a length of at least 8, 12, 20, 25, 50, 75,100, 200, 300, 400, 500, 1000, or more, consecutive nucleotides of thesequence from which it originates.

Specific fragment of an isolated and/or purified nucleotide sequenceaccording to the invention will be understood as designating anynucleotide fragment of the genome of Alicyclobacillus acidocaldarius,having, after alignment and comparison with the corresponding fragmentsof genomic sequences of Alicyclobacillus acidocaldarius, at least onenucleotide or base of different nature.

Homologous isolated and/or purified nucleotide sequence in the sense ofthe present invention is understood as meaning an isolated and/orpurified nucleotide sequence having at least a percentage identity withthe bases of a nucleotide sequence according to the invention of atleast about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, or 99.7%, thispercentage being purely statistical and it being possible to distributethe differences between the two nucleotide sequences at random and overthe whole of their length.

Specific homologous nucleotide sequence in the sense of the presentinvention is understood as meaning a homologous nucleotide sequencehaving at least one nucleotide sequence of a specific fragment, such asdefined above. The “specific” homologous sequences can comprise, forexample, the sequences corresponding to the genomic sequence or to thesequences of its fragments representative of variants of the genome ofAlicyclobacillus acidocaldarius. These specific homologous sequences canthus correspond to variations linked to mutations within strains ofAlicyclobacillus acidocaldarius, and especially correspond totruncations, substitutions, deletions and/or additions of at least onenucleotide. The homologous sequences can likewise correspond tovariations linked to the degeneracy of the genetic code.

The term “degree or percentage of sequence homology” refers to “degreeor percentage of sequence identity between two sequences after optimalalignment” as defined in the present application.

Two amino-acids or nucleotidic sequences are said to be “identical” ifthe sequence of amino-acids or nucleotidic residues, in the twosequences is the same when aligned for maximum correspondence asdescribed below. Sequence comparisons between two (or more) peptides orpolynucleotides are typically performed by comparing sequences of twooptimally aligned sequences over a segment or “comparison window” toidentify and compare local regions of sequence similarity. Optimalalignment of sequences for comparison may be conducted by the localhomology algorithm of Smith and Waterman, Ad. App. Math 2:482 (1981), bythe homology alignment algorithm of Neddleman and Wunsch, J. Mol. Biol.48:443 (1970), by the search for similarity method of Pearson andLipman, Proc. Natl. Acad. Sci. (U.S.A.) 85:2444 (1988), by computerizedimplementation of these algorithms (GAP, BESTFIT, FASTA, and TFASTA inthe Wisconsin Genetics Software Package, Genetics Computer Group (GCG),575 Science Dr., Madison, Wis.), or by visual inspection.

“Percentage of sequence identity” (or degree of identity) is determinedby comparing two optimally aligned sequences over a comparison window,where the portion of the peptide or polynucleotide sequence in thecomparison window may comprise additions or deletions (i.e., gaps) ascompared to the reference sequence (which does not comprise additions ordeletions) for optimal alignment of the two sequences. The percentage iscalculated by determining the number of positions at which the identicalamino-acid residue or nucleic acid base occurs in both sequences toyield the number of matched positions, dividing the number of matchedpositions by the total number of positions in the window of comparisonand multiplying the result by 100 to yield the percentage of sequenceidentity.

The definition of sequence identity given above is the definition thatwould be used by one of skill in the art. The definition by itself doesnot need the help of any algorithm, the algorithms being helpful only toachieve the optimal alignments of sequences, rather than the calculationof sequence identity.

From the definition given above, it follows that there is a well-definedand only one value for the sequence identity between two comparedsequences, which value corresponds to the value obtained for the best oroptimal alignment.

In the BLAST N or BLAST P “BLAST 2 sequence” software, which isavailable at the web site ncbi.nlm.nih.gov/gorf/bl2.html, and habituallyused by the inventors and in general by the skilled person for comparingand determining the identity between two sequences, gap cost whichdepends on the sequence length to be compared is directly selected bythe software (i.e., 11.2 for substitution matrix BLOSUM-62 forlength>85).

Complementary nucleotide sequence of a sequence of the invention isunderstood as meaning any DNA whose nucleotides are complementary tothose of the sequence of the invention, and whose orientation isreversed (antisense sequence).

Hybridization under conditions of stringency with a nucleotide sequenceaccording to the invention is understood as meaning hybridization underconditions of temperature and ionic strength chosen in such a way thatthey allow the maintenance of the hybridization between two fragments ofcomplementary DNA.

By way of illustration, conditions of great stringency of thehybridization step with the aim of defining the nucleotide fragmentsdescribed above are advantageously the following.

The hybridization is carried out at a preferential temperature of 65° C.in the presence of SSC buffer, 1×SSC corresponding to 0.15 M NaCl and0.05 M Na citrate. The washing steps, for example, can be the following:2×SSC, at ambient temperature followed by two washes with 2×SSC, 0.5%SDS at 65° C.; 2×0.5×SSC, 0.5% SDS; at 65° C. for 10 minutes each.

The conditions of intermediate stringency, using, for example, atemperature of 42° C. in the presence of a 2×SSC buffer, or of lessstringency, for example, a temperature of 37° C. in the presence of a2×SSC buffer, respectively require a globally less significantcomplementarity for the hybridization between the two sequences.

The stringent hybridization conditions described above for apolynucleotide with a size of approximately 350 bases will be adapted bya person skilled in the art for oligonucleotides of greater or smallersize, according to the teachings of Sambrook et al., 1989.

Among the isolated and/or purified nucleotide sequences according to theinvention, are those that can be used as a primer or probe in methodsallowing the homologous sequences according to the invention to beobtained, these methods, such as the polymerase chain reaction (PCR),nucleic acid cloning, and sequencing, being well known to a personskilled in the art.

Among the isolated and/or purified nucleotide sequences according to theinvention, those are again preferred that can be used as a primer orprobe in methods allowing the presence of SEQ ID NOS: 2, 19, 36, 53, 70,87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308,325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546,563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, 767, 784,801, 818, 835, 852, 869, 886, 903, 920, 937, 954, 971, 988, 1005, 1022,1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158, 1175, 1192, 1294, 1311,1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447, 1464, 1481, 1498, 1515,1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651, 1668, 1685, 1702, 1719,1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855, 1872, 1889, 1906, 1923,1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059, 2076, 2093, 2110, 2127,2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263, 2280, 2297, 2314, 2331,2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552, 2569, 2603, 2620, 2637,2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773, 2790, 2807, 2824, 2841,2857, 2858, 2860, 2877, 2894, 2911, and 2928, one of their fragments, orone of their variants such as defined below to be diagnosed.

The nucleotide sequence fragments according to the invention can beobtained, for example, by specific amplification, such as PCR, or afterdigestion with appropriate restriction enzymes of nucleotide sequencesaccording to the invention, these methods in particular being describedin the work of Sambrook et al., 1989. Such representative fragments canlikewise be obtained by chemical synthesis according to methods wellknown to persons of ordinary skill in the art.

Modified nucleotide sequence will be understood as meaning anynucleotide sequence obtained by mutagenesis according to techniques wellknown to a person skilled in the art, and containing modifications withrespect to the normal sequences according to the invention, for example,mutations in the regulatory and/or promoter sequences of polypeptideexpression, especially leading to a modification of the rate ofexpression of the polypeptide or to a modulation of the replicativecycle.

Modified nucleotide sequence will likewise be understood as meaning anynucleotide sequence coding for a modified polypeptide, such as definedbelow.

The present invention relates to nucleotide sequence comprising isolatedand/or purified nucleotide sequences of Alicyclobacillus acidocaldarius,characterized in that they are selected from the sequences SEQ ID NOS:2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257,274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495,512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733,750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954, 971,988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158, 1175,1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447, 1464,1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651, 1668,1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855, 1872,1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059, 2076,2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263, 2280,2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552, 2569,2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773, 2790,2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and 2928 or one oftheir fragments.

Embodiments of the invention likewise relate to isolated and/or purifiednucleotide sequences characterized in that they comprise a nucleotidesequence selected from: a) at least one of a nucleotide sequence of SEQID NOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223,240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461,478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699,716, 733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937,954, 971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141,1158, 1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430,1447, 1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634,1651, 1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838,1855, 1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042,2059, 2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246,2263, 2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535,2552, 2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756,2773, 2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and2928 or one of their fragments; b) a nucleotide sequence of a specificfragment of a sequence such as defined in a); c) a homologous nucleotidesequence having at least 80% identity with a sequence such as defined ina) or b); d) a complementary nucleotide sequence or sequence of RNAcorresponding to a sequence such as defined in a), b) or c); and e) anucleotide sequence modified by a sequence such as defined in a), b), c)or d).

Among the isolated and/or purified nucleotide sequences according to theinvention are the nucleotide sequences of SEQ ID NOS: 13-17, 30-34,47-51, 64-68, 81-85, 98-102, 115-119, 132-136, 149-153, 166-170,183-187, 200-204, 217-221, 234-238, 251-255, 268-272, 285-289, 302-306,319-323, 336-340, 353-357, 370-374, 387-391, 404-408, 421-425, 438-442,455-459, 472-476, 489-493, 506-510, 523-527, 540-544, 557-561, 574-578,591-595, 608-612, 625-629, 642-646, 659-663, 676-680, 693-697, 710-714,727-731, 744-748, 761-765, 778-782, 795-799, 812-816, 829-833, 846-850,863-867, 880-884, 897-901, 914-918, 931-935, 948-952, 965-969, 982-986,999-1003, 1016-1020, 1033-1037, 1050-1054, 1067-1071, 1084-1088,1101-1105, 1118-1122, 1135-1139, 1152-1156, 1169-1173, 1186-1190,1203-1207, 1305-1309, 1322-1326, 1339-1343, 1356-1360, 1373-1377,1390-1394, 1407-1411, 1424-1428, 1441-1445, 1458-1462, 1475-1479,1492-1496, 1509-1513, 1526-1530, 1543-1547, 1560-1564, 1577-1581,1594-1598, 1611-1615, 1628-1632, 1645-1649, 1662-1666, 1679-1683,1696-1700, 1713-1717, 1730-1734, 1747-1751, 1764-1768, 1781-1785,1798-1802, 1815-1819, 1832-1836, 1849-1853, 1866-1870, 1883-1887,1900-1904, 1917-1921, 1934-1938, 1951-1955, 1968-1972, 1985-1989,2002-2006, 2019-2023, 2036-2040, 2053-2057, 2070-2074, 2087-2091,2104-2108, 2121-2125, 2138-2142, 2155-2159, 2172-2176, 2189-2193,2206-2210, 2223-2227, 2240-2244, 2257-2261, 2274-2278, 2291-2295,2308-2312, 2325-2329, 2342-2346, 2359-2363, 2376-2380, 2393-2397,2410-2414, 2427-2431, 2529-2533, 2546-2550, 2563-2567, 2580-2584,2614-2618, 2631-2635, 2648-2652, 2665-2669, 2682-2686, 2699-2703,2716-2720, 2733-2737, 2750-2754, 2767-2771, 2784-2788, 2801-2805,2818-2822, 2835-2839, 2852-2856, 2878-2882, 2888-2892, 2905-2909,2922-2926, and 2939-2943, or fragments thereof and any isolated and/orpurified nucleotide sequences which have a homology of at least 80%,81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, or 99.7% identity with the atleast one of the sequences of SEQ ID NOS: 2, 19, 36, 53, 70, 87, 104,121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342,359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580,597, 614, 631, 648, 665, 682, 699, 716, 733, 750, 767, 784, 801, 818,835, 852, 869, 886, 903, 920, 937, 954, 971, 988, 1005, 1022, 1039,1056, 1073, 1090, 1107, 1124, 1141, 1158, 1175, 1192, 1294, 1311, 1328,1345, 1362, 1379, 1396, 1413, 1430, 1447, 1464, 1481, 1498, 1515, 1532,1549, 1566, 1583, 1600, 1617, 1634, 1651, 1668, 1685, 1702, 1719, 1736,1753, 1770, 1787, 1804, 1821, 1838, 1855, 1872, 1889, 1906, 1923, 1940,1957, 1974, 1991, 2008, 2025, 2042, 2059, 2076, 2093, 2110, 2127, 2144,2161, 2178, 2195, 2212, 2229, 2246, 2263, 2280, 2297, 2314, 2331, 2348,2365, 2382, 2399, 2416, 2518, 2535, 2552, 2569, 2603, 2620, 2637, 2654,2671, 2688, 2705, 2722, 2739, 2756, 2773, 2790, 2807, 2824, 2841, 2857,2858, 2860, 2877, 2894, 2911, and 2928 or fragments thereof. Thehomologous sequences can comprise, for example, the sequencescorresponding to the genomic sequences Alicyclobacillus acidocaldarius.In the same manner, these specific homologous sequences can correspondto variations linked to mutations within strains of Alicyclobacillusacidocaldarius and especially correspond to truncations, substitutions,deletions and/or additions of at least one nucleotide. As will beapparent to one of ordinary skill in the art, such homologues are easilycreated and identified using standard techniques and publicly availablecomputer programs such as BLAST. As such, each homologue referencedabove should be considered as set forth herein and fully described.

Embodiments of the invention comprise the isolated and/or purifiedpolypeptides coded for by a nucleotide sequence according to theinvention, or fragments thereof, whose sequence is represented by afragment. Amino acid sequences corresponding to the isolated and/orpurified polypeptides which can be coded for according to one of thethree possible reading frames of at least one of the sequences of SEQ IDNOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240,257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478,495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716,733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954,971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158,1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447,1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651,1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855,1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059,2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263,2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552,2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773,2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and 2928.

Embodiments of the invention likewise relate to the isolated and/orpurified polypeptides, characterized in that they comprise a polypeptideselected from at least one of the amino acid sequences of SEQ ID NOS: 1,18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256,273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494,511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732,749, 766, 783, 800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970,987, 1004, 1021, 1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174,1191, 1293, 1310, 1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463,1480, 1497, 1514, 1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667,1684, 1701, 1718, 1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871,1888, 1905, 1922, 1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075,2092, 2109, 2126, 2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279,2296, 2313, 2330, 2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568,2602, 2619, 2636, 2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789,2806, 2823, 2840, 2859, 2876, 2893, 2910, and 2927 or one of theirfragments.

Among the isolated and/or purified polypeptides, according toembodiments of the invention, are the isolated and/or purifiedpolypeptides of amino acid sequence SEQ ID NOS: 8-12, 25-29, 42-46,59-63, 76-80, 93-97, 110-114, 127-131, 144-148, 161-165, 178-182,195-199, 212-216, 229-233, 246-250, 263-267, 280-284, 297-301, 314-318,331-335, 348-352, 365-369, 382-386, 399-403, 416-420, 433-437, 450-454,467-471, 484-488, 501-505, 518-522, 535-539, 552-556, 569-573, 586-590,603-607, 620-624, 637-641, 654-658, 671-675, 688-692, 705-709, 722-726,739-743, 756-760, 773-777, 790-794, 807-811, 824-828, 841-845, 858-862,875-879, 892-896, 909-913, 926-930, 943-947, 960-964, 977-981, 994-998,1011-1015, 1028-1032, 1045-1049, 1062-1066, 1079-1083, 1096-1100,1113-1117, 1130-1134, 1147-1151, 1164-1168, 1181-1185, 1198-1202,1300-1304, 1317-1321, 1334-1338, 1351-1355, 1368-1372, 1385-1389,1402-1406, 1419-1423, 1436-1440, 1453-1457, 1470-1474, 1487-1491,1504-1508, 1521-1525, 1538-1542, 1555-1559, 1572-1576, 1589-1593,1606-1610, 1623-1627, 1640-1644, 1657-1661, 1674-1678, 1691-1695,1708-1712, 1725-1729, 1742-1746, 1759-1763, 1776-1780, 1793-1797,1810-1814, 1827-1831, 1844-1848, 1861-1865, 1878-1882, 1895-1899,1912-1916, 1929-1933, 1946-1950, 1963-1967, 1980-1984, 1997-2001,2014-2018, 2031-2035, 2048-2052, 2065-2069, 2082-2086, 2099-2103,2116-2120, 2133-2137, 2150-2154, 2167-2171, 2184-2188, 2201-2205,2218-2222, 2235-2239, 2252-2256, 2269-2273, 2286-2290, 2303-2307,2320-2324, 2337-2341, 2354-2358, 2371-2375, 2388-2392, 2405-2409,2422-2426, 2524-2528, 2541-2545, 2558-2562, 2575-2579, 2609-2613,2626-2630, 2643-2647, 2660-2664, 2677-2681, 2694-2698, 2711-2715,2728-2732, 2745-2749, 2762-2766, 2779-2783, 2796-2800, 2813-2817,2830-2834, 2847-2851, 2866-2870, 2883-2887, 2900-2914, 2917-2921, and2934-2938, or fragments thereof or any other isolated and/or purifiedpolypeptides which have a homology of at least 80%, 81%, 82%, 83%, 84%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, 99.5%, 99.6%, or 99.7% identity with at least one of the sequencesof SEQ ID NOS: 1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205,222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443,460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681,698, 715, 732, 749, 766, 783, 800, 817, 834, 851, 868, 885, 902, 819,936, 953, 970, 987, 1004, 1021, 1038, 1055, 1072, 1089, 1106, 1123,1140, 1157, 1174, 1191, 1293, 1310, 1327, 1344, 1361, 1378, 1395, 1412,1429, 1446, 1463, 1480, 1497, 1514, 1531, 1548, 1565, 1582, 1599, 1616,1633, 1650, 1667, 1684, 1701, 1718, 1735, 1752, 1769, 1786, 1803, 1820,1837, 1854, 1871, 1888, 1905, 1922, 1939, 1956, 1973, 1990, 2007, 2024,2041, 2058, 2075, 2092, 2109, 2126, 2143, 2160, 2177, 2194, 2211, 2228,2245, 2262, 2279, 2296, 2313, 2330, 2347, 2364, 2381, 2398, 2415, 2517,2534, 2551, 2568, 2602, 2619, 2636, 2653, 2670, 2687, 2704, 2721, 2738,2755, 2772, 2789, 2806, 2823, 2840, 2859, 2876, 2893, 2910, and 2927 orfragments thereof. As will be apparent to one of ordinary skill in theart, such homologues are easily created and identified using standardtechniques and publicly available computer programs such as BLAST. Assuch, each homologue referenced above should be considered as set forthherein and fully described.

Embodiments of the invention also relate to the polypeptides,characterized in that they comprise a polypeptide selected from: a) aspecific fragment of at least 5 amino acids of a polypeptide of an aminoacid sequence according to the invention; b) a polypeptide homologous toa polypeptide such as defined in a); c) a specific biologically activefragment of a polypeptide such as defined in a) or b); and d) apolypeptide modified by a polypeptide such as defined in a), b) or c).

In the present description, the terms polypeptide, peptide and proteinare interchangeable.

In embodiments of the invention, the isolated and/or purifiedpolypeptides according to the invention may be glycosylated, pegylated,and/or otherwise post-translationally modified. In further embodiments,glycosylation, pegylation, and/or other post-translational modificationsmay occur in vivo or in vitro and/or may be performed using chemicaltechniques. In additional embodiments, any glycosylation, pegylationand/or other post-translational modifications may be N-linked orO-linked.

In embodiments of the invention any one of the isolated and/or purifiedpolypeptides according to the invention may be enzymatically orfunctionally active at temperatures at or above about 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/ormay be enzymatically or functionally active at a pH at, below, and/orabove 8, 7, 6, 5, 4, 3, 2, 1, and/or 0. In further embodiments of theinvention, glycosylation, pegylation, and/or other post-translationalmodification may be required for the isolated and/or purifiedpolypeptides according to the invention to be enzymatically orfunctionally active at a pH at or below 8, 7, 6, 5, 4, 3, 2, 1, and/or 0or at temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65,70, 75, 80, 85, 90, and/or 95 degrees Celsius.

Aspects of the invention relate to polypeptides that are isolated orobtained by purification from natural sources, or else obtained bygenetic recombination, or alternatively by chemical synthesis and thatthey may thus contain unnatural amino acids, as will be described below.

A “polypeptide fragment” according to the embodiments of the inventionis understood as designating a polypeptide containing at least 5consecutive amino acids, preferably 10 consecutive amino acids or 15consecutive amino acids.

In the present invention, a specific polypeptide fragment is understoodas designating the consecutive polypeptide fragment coded for by aspecific fragment nucleotide sequence according to the invention.

“Homologous polypeptide” will be understood as designating thepolypeptides having, with respect to the natural polypeptide, certainmodifications such as, in particular, a deletion, addition, orsubstitution of at least one amino acid, a truncation, a prolongation, achimeric fusion, and/or a mutation. Among the homologous polypeptides,those are preferred whose amino acid sequence has at least 80% or 90%,homology with the sequences of amino acids of polypeptides according tothe invention.

“Specific homologous polypeptide” will be understood as designating thehomologous polypeptides such as defined above and having a specificfragment of polypeptide according to the invention.

In the case of a substitution, one or more consecutive or nonconsecutiveamino acids are replaced by “equivalent” amino acids. The expression“equivalent” amino acid is directed here at designating any amino acidcapable of being substituted by one of the amino acids of the basestructure without, however, essentially modifying the biologicalactivities of the corresponding peptides and such that they will bedefined by the following. As will be apparent to one of ordinary skillin the art, such substitutions are easily created and identified usingstandard molecular biology techniques and publicly available computerprograms such as BLAST. As such, each substitution referenced aboveshould be considered as set forth herein and fully described. Examplesof such substitutions in the amino acid sequences SEQ ID NOS: 1, 18, 35,52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290,307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528,545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766,783, 800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004,1021, 1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293,1310, 1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497,1514, 1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701,1718, 1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905,1922, 1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109,2126, 2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313,2330, 2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619,2636, 2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823,2840, 2859, 2876, 2893, 2910, and 2927 may include those isolated and/orpurified polypeptides of amino acid sequence SEQ ID NOS: 8-12, 25-29,42-46, 59-63, 76-80, 93-97, 110-114, 127-131, 144-148, 161-165, 178-182,195-199, 212-216, 229-233, 246-250, 263-267, 280-284, 297-301, 314-318,331-335, 348-352, 365-369, 382-386, 399-403, 416-420, 433-437, 450-454,467-471, 484-488, 501-505, 518-522, 535-539, 552-556, 569-573, 586-590,603-607, 620-624, 637-641, 654-658, 671-675, 688-692, 705-709, 722-726,739-743, 756-760, 773-777, 790-794, 807-811, 824-828, 841-845, 858-862,875-879, 892-896, 909-913, 926-930, 943-947, 960-964, 977-981, 994-998,1011-1015, 1028-1032, 1045-1049, 1062-1066, 1079-1083, 1096-1100,1113-1117, 1130-1134, 1147-1151, 1164-1168, 1181-1185, 1198-1202,1300-1304, 1317-1321, 1334-1338, 1351-1355, 1368-1372, 1385-1389,1402-1406, 1419-1423, 1436-1440, 1453-1457, 1470-1474, 1487-1491,1504-1508, 1521-1525, 1538-1542, 1555-1559, 1572-1576, 1589-1593,1606-1610, 1623-1627, 1640-1644, 1657-1661, 1674-1678, 1691-1695,1708-1712, 1725-1729, 1742-1746, 1759-1763, 1776-1780, 1793-1797,1810-1814, 1827-1831, 1844-1848, 1861-1865, 1878-1882, 1895-1899,1912-1916, 1929-1933, 1946-1950, 1963-1967, 1980-1984, 1997-2001,2014-2018, 2031-2035, 2048-2052, 2065-2069, 2082-2086, 2099-2103,2116-2120, 2133-2137, 2150-2154, 2167-2171, 2184-2188, 2201-2205,2218-2222, 2235-2239, 2252-2256, 2269-2273, 2286-2290, 2303-2307,2320-2324, 2337-2341, 2354-2358, 2371-2375, 2388-2392, 2405-2409,2422-2426, 2524-2528, 2541-2545, 2558-2562, 2575-2579, 2609-2613,2626-2630, 2643-2647, 2660-2664, 2677-2681, 2694-2698, 2711-2715,2728-2732, 2745-2749, 2762-2766, 2779-2783, 2796-2800, 2813-2817,2830-2834, 2847-2851, 2866-2870, 2883-2887, 2900-2914, 2917-2921, and2934-2938.

These equivalent amino acids can be determined either by depending ontheir structural homology with the amino acids, which they substitute,or on results of comparative tests of biological activity between thedifferent polypeptides, which are capable of being carried out.

By way of non-limiting example, the possibilities of substitutionscapable of being carried out without resulting in an extensivemodification of the biological activity of the corresponding modifiedpolypeptides will be mentioned, the replacement, for example, of leucineby valine or isoleucine, of aspartic acid by glutamic acid, of glutamineby asparagine, of arginine by lysine, etc., the reverse substitutionsnaturally being envisageable under the same conditions.

In a further embodiment, substitutions are limited to substitutions inamino acids not conserved among other proteins which have similaridentified activity. For example, one of ordinary skill in the art mayalign proteins of the same function in similar organisms and determinewhich amino acids are generally conserved among proteins of thatfunction. One example of a program that may be used to generate suchalignments is available at the website charite.de/bioinf/strap/ inconjunction with the databases provided by the NCBI. Examples of suchpolypeptides may include, but are not limited to, those found in aminoacid sequence SEQ ID NOS: 8-12, 25-29, 42-46, 59-63, 76-80, 93-97,110-114, 127-131, 144-148, 161-165, 178-182, 195-199, 212-216, 229-233,246-250, 263-267, 280-284, 297-301, 314-318, 331-335, 348-352, 365-369,382-386, 399-403, 416-420, 433-437, 450-454, 467-471, 484-488, 501-505,518-522, 535-539, 552-556, 569-573, 586-590, 603-607, 620-624, 637-641,654-658, 671-675, 688-692, 705-709, 722-726, 739-743, 756-760, 773-777,790-794, 807-811, 824-828, 841-845, 858-862, 875-879, 892-896, 909-913,926-930, 943-947, 960-964, 977-981, 994-998, 1011-1015, 1028-1032,1045-1049, 1062-1066, 1079-1083, 1096-1100, 1113-1117, 1130-1134,1147-1151, 1164-1168, 1181-1185, 1198-1202, 1300-1304, 1317-1321,1334-1338, 1351-1355, 1368-1372, 1385-1389, 1402-1406, 1419-1423,1436-1440, 1453-1457, 1470-1474, 1487-1491, 1504-1508, 1521-1525,1538-1542, 1555-1559, 1572-1576, 1589-1593, 1606-1610, 1623-1627,1640-1644, 1657-1661, 1674-1678, 1691-1695, 1708-1712, 1725-1729,1742-1746, 1759-1763, 1776-1780, 1793-1797, 1810-1814, 1827-1831,1844-1848, 1861-1865, 1878-1882, 1895-1899, 1912-1916, 1929-1933,1946-1950, 1963-1967, 1980-1984, 1997-2001, 2014-2018, 2031-2035,2048-2052, 2065-2069, 2082-2086, 2099-2103, 2116-2120, 2133-2137,2150-2154, 2167-2171, 2184-2188, 2201-2205, 2218-2222, 2235-2239,2252-2256, 2269-2273, 2286-2290, 2303-2307, 2320-2324, 2337-2341,2354-2358, 2371-2375, 2388-2392, 2405-2409, 2422-2426, 2524-2528,2541-2545, 2558-2562, 2575-2579, 2609-2613, 2626-2630, 2643-2647,2660-2664, 2677-2681, 2694-2698, 2711-2715, 2728-2732, 2745-2749,2762-2766, 2779-2783, 2796-2800, 2813-2817, 2830-2834, 2847-2851,2866-2870, 2883-2887, 2900-2914, 2917-2921, and 2934-2938.

Thus, according to one embodiment of the invention, substitutions ormutations may be made at positions that are generally conserved amongproteins of that function. In a further embodiment, nucleic acidsequences may be mutated or substituted such that the amino acid theycode for is unchanged (degenerate substitutions and/or mutations) and/ormutated or substituted such that any resulting amino acid substitutionsor mutations are made at positions that are generally conserved amongproteins of that function. Examples of such nucleic acid sequences mayinclude, but are not limited to, those found in are the nucleotidesequences of SEQ ID NOS: 13-17, 30-34, 47-51, 64-68, 81-85, 98-102,115-119, 132-136, 149-153, 166-170, 183-187, 200-204, 217-221, 234-238,251-255, 268-272, 285-289, 302-306, 319-323, 336-340, 353-357, 370-374,387-391, 404-408, 421-425, 438-442, 455-459, 472-476, 489-493, 506-510,523-527, 540-544, 557-561, 574-578, 591-595, 608-612, 625-629, 642-646,659-663, 676-680, 693-697, 710-714, 727-731, 744-748, 761-765, 778-782,795-799, 812-816, 829-833, 846-850, 863-867, 880-884, 897-901, 914-918,931-935, 948-952, 965-969, 982-986, 999-1003, 1016-1020, 1033-1037,1050-1054, 1067-1071, 1084-1088, 1101-1105, 1118-1122, 1135-1139,1152-1156, 1169-1173, 1186-1190, 1203-1207, 1305-1309, 1322-1326,1339-1343, 1356-1360, 1373-1377, 1390-1394, 1407-1411, 1424-1428,1441-1445, 1458-1462, 1475-1479, 1492-1496, 1509-1513, 1526-1530,1543-1547, 1560-1564, 1577-1581, 1594-1598, 1611-1615, 1628-1632,1645-1649, 1662-1666, 1679-1683, 1696-1700, 1713-1717, 1730-1734,1747-1751, 1764-1768, 1781-1785, 1798-1802, 1815-1819, 1832-1836,1849-1853, 1866-1870, 1883-1887, 1900-1904, 1917-1921, 1934-1938,1951-1955, 1968-1972, 1985-1989, 2002-2006, 2019-2023, 2036-2040,2053-2057, 2070-2074, 2087-2091, 2104-2108, 2121-2125, 2138-2142,2155-2159, 2172-2176, 2189-2193, 2206-2210, 2223-2227, 2240-2244,2257-2261, 2274-2278, 2291-2295, 2308-2312, 2325-2329, 2342-2346,2359-2363, 2376-2380, 2393-2397, 2410-2414, 2427-2431, 2529-2533,2546-2550, 2563-2567, 2580-2584, 2614-2618, 2631-2635, 2648-2652,2665-2669, 2682-2686, 2699-2703, 2716-2720, 2733-2737, 2750-2754,2767-2771, 2784-2788, 2801-2805, 2818-2822, 2835-2839, 2852-2856,2878-2882, 2888-2892, 2905-2909, 2922-2926, and 2939-2943 or fragmentsthereof.

The specific homologous polypeptides likewise correspond to polypeptidescoded for by the specific homologous nucleotide sequences such asdefined above and thus comprise in the present definition thepolypeptides, which are mutated or correspond to variants that can existin Alicyclobacillus acidocaldarius, and which especially correspond totruncations, substitutions, deletions, and/or additions of at least oneamino acid residue.

“Specific biologically active fragment of a polypeptide” according to anembodiment of the invention will be understood in particular asdesignating a specific polypeptide fragment, such as defined above,having at least one of the characteristics of polypeptides according tothe invention. In certain embodiments the peptide is capable of behavingas at least one of the types of proteins outlined in Table 1.

The polypeptide fragments according to embodiments of the invention cancorrespond to isolated or purified fragments naturally present inAlicyclobacillus acidocaldarius or correspond to fragments that can beobtained by cleavage of the polypeptide by a proteolytic enzyme, such astrypsin or chymotrypsin or collagenase, or by a chemical reagent, suchas cyanogen bromide (CNBr). Such polypeptide fragments can likewise justas easily be prepared by chemical synthesis, from hosts transformed byan expression vector according to the invention containing a nucleicacid allowing the expression of the fragments, placed under the controlof appropriate regulation and/or expression elements.

“Modified polypeptide” of a polypeptide according to an embodiment ofthe invention is understood as designating a polypeptide obtained bygenetic recombination or by chemical synthesis as will be describedbelow, having at least one modification with respect to the normalsequence. These modifications may or may not be able to bear on aminoacids at the origin of specificity, and/or of activity, or at the originof the structural conformation, localization, and of the capacity ofmembrane insertion of the polypeptide according to the invention. Itwill thus be possible to create polypeptides of equivalent, increased,or decreased activity, and of equivalent, narrower, or widerspecificity. Among the modified polypeptides, it is necessary to mentionthe polypeptides in which up to 5 or more amino acids can be modified,truncated at the N- or C-terminal end, or even deleted or added.

The methods allowing the modulations on eukaryotic or prokaryotic cellsto be demonstrated are well known to a person of ordinary skill in theart. It is likewise well understood that it will be possible to use thenucleotide sequences coding for the modified polypeptides for themodulations, for example, through vectors according to the invention anddescribed below.

The preceding modified polypeptides can be obtained by usingcombinatorial chemistry, in which it is possible to systematically varyparts of the polypeptide before testing them on models, cell cultures ormicroorganisms, for example, to select the compounds that are mostactive or have the properties sought.

Chemical synthesis likewise has the advantage of being able to useunnatural amino acids, or nonpeptide bonds.

Thus, in order to improve the duration of life of the polypeptides,according to the invention, it may be of interest to use unnatural aminoacids, for example, in D form, or else amino acid analogs, especiallysulfur-containing forms, for example.

Finally, it will be possible to integrate the structure of thepolypeptides according to the invention, its specific or modifiedhomologous forms, into chemical structures of polypeptide type orothers. Thus, it may be of interest to provide at the N- and C-terminalends compounds not recognized by proteases.

The nucleotide sequences coding for a polypeptide according to theinvention are likewise part of the invention.

The invention likewise relates to nucleotide sequences utilizable as aprimer or probe, characterized in that the sequences are selected fromthe nucleotide sequences according to the invention.

It is well understood that the present invention, in variousembodiments, likewise relates to specific polypeptides ofAlicyclobacillus acidocaldarius, coded for by nucleotide sequences,capable of being obtained by purification from natural polypeptides, bygenetic recombination or by chemical synthesis by procedures well knownto a person skilled in the art and such as described in particularbelow. In the same manner, the labeled or unlabeled mono- or polyclonalantibodies directed against the specific polypeptides coded for by thenucleotide sequences are also encompassed by the invention.

Embodiments of the invention additionally relate to the use of anucleotide sequence according to the invention as a primer or probe forthe detection and/or the amplification of nucleic acid sequences.

The nucleotide sequences according to embodiments of the invention canthus be used to amplify nucleotide sequences, especially by the PCRtechnique (polymerase chain reaction) (Erlich, 1989; Innis et al., 1990;Rolfs et al., 1991; and White et al., 1997).

These oligodeoxyribonucleotide or oligoribonucleotide primersadvantageously have a length of at least 8 nucleotides, preferably of atleast 12 nucleotides, and even more preferentially of at least 20nucleotides.

Other amplification techniques of the target nucleic acid can beadvantageously employed as alternatives to PCR.

The nucleotide sequences of the invention, in particular the primersaccording to the invention, can likewise be employed in other proceduresof amplification of a target nucleic acid, such as: the TAS technique(Transcription-based Amplification System), described by Kwoh et al. in1989; the 3SR technique (Self-Sustained Sequence Replication), describedby Guatelli et al. in 1990; the NASBA technique (Nucleic Acid SequenceBased Amplification), described by Kievitis et al. in 1991; the SDAtechnique (Strand Displacement Amplification) (Walker et al., 1992); andthe TMA technique (Transcription Mediated Amplification).

The polynucleotides of the invention can also be employed in techniquesof amplification or of modification of the nucleic acid serving as aprobe, such as: the LCR technique (Ligase Chain Reaction), described byLandegren et al. in 1988 and improved by Barany et al. in 1991, whichemploys a thermostable ligase; the RCR technique (Repair ChainReaction), described by Segev in 1992; the CPR technique (Cycling ProbeReaction), described by Duck et al. in 1990; the amplification techniquewith Q-beta replicase, described by Miele et al. in 1983 and especiallyimproved by Chu et al. in 1986, Lizardi et al. in 1988, then by Burg etal., as well as by Stone et al. in 1996.

In the case where the target polynucleotide to be detected is possiblyan RNA, for example, an mRNA, it will be possible to use, prior to theemployment of an amplification reaction with the aid of at least oneprimer according to the invention or to the employment of a detectionprocedure with the aid of at least one probe of the invention, an enzymeof reverse transcriptase type in order to obtain a cDNA from the RNAcontained in the biological sample. The cDNA obtained will thus serve asa target for the primer(s) or the probe(s) employed in the amplificationor detection procedure according to the invention.

The detection probe will be chosen in such a manner that it hybridizeswith the target sequence or the amplicon generated from the targetsequence. By way of sequence, such a probe will advantageously have asequence of at least 12 nucleotides, in particular of at least 20nucleotides, and preferably of at least 100 nucleotides.

Embodiments of the invention also comprise the nucleotide sequencesutilizable as a probe or primer according to the invention,characterized in that they are labeled with a radioactive compound orwith a nonradioactive compound.

The unlabeled nucleotide sequences can be used directly as probes orprimers, although the sequences are generally labeled with a radioactiveisotope (³²P, ³⁵S, ³H, ¹²⁵I) or with a nonradioactive molecule (biotin,acetylaminofluorene, digoxigenin, 5-bromodeoxyuridine, fluorescein) toobtain probes, which are utilizable for numerous applications.

Examples of nonradioactive labeling of nucleotide sequences aredescribed, for example, in French Patent No. 7810975 or by Urdea et al.or by Sanchez-Pescador et al. in 1988.

In the latter case, it will also be possible to use one of the labelingmethods described in patents FR-2 422 956 and FR-2 518 755.

The hybridization technique can be carried out in various manners(Matthews et al., 1988). The most general method consists inimmobilizing the nucleic acid extract of cells on a support (such asnitrocellulose, nylon, polystyrene) and in incubating, underwell-defined conditions, the immobilized target nucleic acid with theprobe. After hybridization, the excess of probe is eliminated and thehybrid molecules formed are detected by the appropriate method(measurement of the radioactivity, of the fluorescence or of theenzymatic activity linked to the probe).

The invention, in various embodiments, likewise comprises the nucleotidesequences according to the invention, characterized in that they areimmobilized on a support, covalently or noncovalently.

According to another advantageous mode of employing nucleotide sequencesaccording to the invention, the latter can be used immobilized on asupport and can thus serve to capture, by specific hybridization, thetarget nucleic acid obtained from the biological sample to be tested. Ifnecessary, the solid support is separated from the sample and thehybridization complex formed between the capture probe and the targetnucleic acid is then detected with the aid of a second probe, aso-called detection probe, labeled with an easily detectable element.

Another aspect of the present invention is a vector for the cloningand/or expression of a sequence, characterized in that it contains anucleotide sequence according to the invention.

The vectors, according to the invention, characterized in that theycontain the elements allowing the integration, expression and/or thesecretion of the nucleotide sequences in a determined host cell, arelikewise part of the invention.

The vector may then contain a promoter, signals of initiation andtermination of translation, as well as appropriate regions of regulationof transcription. It may be able to be maintained stably in the hostcell and can optionally have particular signals specifying the secretionof the translated protein. These different elements may be chosen as afunction of the host cell used. To this end, the nucleotide sequencesaccording to the invention may be inserted into autonomous replicationvectors within the chosen host, or integrated vectors of the chosenhost.

Such vectors will be prepared according to the methods currently used bya person skilled in the art, and it will be possible to introduce theclones resulting therefrom into an appropriate host by standard methods,such as, for example, lipofection, electroporation, and thermal shock.

The vectors according to the invention are, for example, vectors ofplasmid or viral origin. One example of a vector for the expression ofpolypeptides of the invention is Baculovirus.

These vectors are useful for transforming host cells in order to cloneor to express the nucleotide sequences of the invention.

The invention likewise comprises the host cells transformed by a vectoraccording to the invention.

These cells can be obtained by the introduction into host cells of anucleotide sequence inserted into a vector such as defined above, thenthe culturing of the cells under conditions allowing the replicationand/or expression of the transfected nucleotide sequence.

The host cell can be selected from prokaryotic or eukaryotic systems,such as, for example, bacterial cells (Olins and Lee, 1993), butlikewise yeast cells (Buckholz, 1993), as well as plants cells, such asArabidopsis sp., and animal cells, in particular the cultures ofmammalian cells (Edwards and Aruffo, 1993), for example, Chinese hamsterovary (CHO) cells, but likewise the cells of insects in which it ispossible to use procedures employing baculoviruses, for example, Sf9insect cells (Luckow, 1993).

Embodiments of the invention likewise relate to organisms comprising oneof the transformed cells according to the invention.

The obtainment of transgenic organisms, according to the invention, ofexpressing one or more of the genes of Alicyclobacillus acidocaldariusor part of the genes may be carried out in, for example, rats, mice, orrabbits according to methods well known to a person skilled in the art,such as by viral or nonviral transfections. It will be possible toobtain the transgenic organisms expressing one or more of the genes bytransfection of multiple copies of the genes under the control of astrong promoter of ubiquitous nature, or selective for one type oftissue. It will likewise be possible to obtain the transgenic organismsby homologous recombination in embryonic cell strains, transfer of thesecell strains to embryos, selection of the affected chimeras at the levelof the reproductive lines, and growth of the chimeras.

The transformed cells, as well as the transgenic organisms according tothe invention, are utilizable in procedures for preparation ofrecombinant polypeptides.

It is today possible to produce recombinant polypeptides in relativelylarge quantity by genetic engineering using the cells transformed byexpression vectors according to the invention or using transgenicorganisms according to the invention.

The procedures for preparation of a polypeptide of the invention inrecombinant form, characterized in that they employ a vector and/or acell transformed by a vector according to the invention and/or atransgenic organism comprising one of the transformed cells according tothe invention are themselves comprised in the present invention.

As used herein, “transformation” and “transformed” relate to theintroduction of nucleic acids into a cell, whether prokaryotic oreukaryotic. Further, “transformation” and “transformed,” as used herein,need not relate to growth control or growth deregulation.

Among the procedures for preparation of a polypeptide of the inventionin recombinant form, the preparation procedures employing a vector,and/or a cell transformed by the vector and/or a transgenic organismcomprising one of the transformed cells, containing a nucleotidesequence according to the invention coding for a polypeptide ofAlicyclobacillus acidocaldarius.

A variant according to the invention may consist of producing arecombinant polypeptide fused to a “carrier” protein (chimeric protein).The advantage of this system is that it may allow stabilization ofand/or a decrease in the proteolysis of the recombinant product, anincrease in the solubility in the course of renaturation in vitro and/ora simplification of the purification when the fusion partner has anaffinity for a specific ligand.

More particularly, the invention relates to a procedure for preparationof a polypeptide of the invention comprising the following steps: a)culture of transformed cells under conditions allowing the expression ofa recombinant polypeptide of a nucleotide sequence according to theinvention; b) if need be, recovery of the recombinant polypeptide.

When the procedure for preparation of a polypeptide of the inventionemploys a transgenic organism according to the invention, therecombinant polypeptide is then extracted from the organism.

The invention also relates to a polypeptide that is capable of beingobtained by a procedure of the invention, such as described previously.

The invention also comprises a procedure for preparation of a syntheticpolypeptide, characterized in that it uses a sequence of amino acids ofpolypeptides according to the invention.

The invention likewise relates to a synthetic polypeptide obtained by aprocedure according to the invention.

The polypeptides according to the invention can likewise be prepared bytechniques that are conventional in the field of the synthesis ofpeptides. This synthesis can be carried out in homogeneous solution orin solid phase.

For example, recourse can be made to the technique of synthesis in ahomogeneous solution described by Houben-Weyl in 1974.

This method of synthesis consists in successively condensing, two bytwo, the successive amino acids in the order required, or in condensingamino acids and fragments formed previously and already containingseveral amino acids in the appropriate order, or alternatively severalfragments previously prepared in this way, it being understood that itwill be necessary to protect beforehand all the reactive functionscarried by these amino acids or fragments, with the exception of aminefunctions of one and carboxyls of the other or vice-versa, which mustnormally be involved in the formation of peptide bonds, especially afteractivation of the carboxyl function, according to the methods well knownin the synthesis of peptides.

Recourse may also be made to the technique described by Merrifield.

To make a peptide chain according to the Merrifield procedure, recourseis made to a very porous polymeric resin, on which is immobilized thefirst C-terminal amino acid of the chain. This amino acid is immobilizedon a resin through its carboxyl group and its amine function isprotected. The amino acids that are going to form the peptide chain arethus immobilized, one after the other, on the amino group, which isdeprotected beforehand each time, of the portion of the peptide chainalready formed, and which is attached to the resin. When the whole ofthe desired peptide chain has been formed, the protective groups of thedifferent amino acids forming the peptide chain are eliminated and thepeptide is detached from the resin with the aid of an acid.

The invention additionally relates to hybrid polypeptides having atleast one polypeptide according to the invention, and a sequence of apolypeptide capable of inducing an immune response in man or animals.

Advantageously, the antigenic determinant is such that it is capable ofinducing a humoral and/or cellular response.

It will be possible for such a determinant to comprise a polypeptideaccording to the invention in glycosylated, pegylated, and/or otherwisepost-translationally modified form used with a view to obtainingimmunogenic compositions capable of inducing the synthesis of antibodiesdirected against multiple epitopes.

These hybrid molecules can be formed, in part, of a polypeptide carriermolecule or of fragments thereof according to the invention, associatedwith a possibly immunogenic part, in particular, an epitope of thediphtheria toxin, the tetanus toxin, a surface antigen of the hepatitisB virus (Patent FR 79 21811), the VP1 antigen of the poliomyelitis virusor any other viral or bacterial toxin or antigen.

The procedures for synthesis of hybrid molecules encompass the methodsused in genetic engineering for constructing hybrid nucleotide sequencescoding for the polypeptide sequences sought. It will be possible, forexample, to refer advantageously to the technique for obtainment ofgenes coding for fusion proteins described by Minton in 1984.

The hybrid nucleotide sequences coding for a hybrid polypeptide as wellas the hybrid polypeptides according to the invention characterized inthat they are recombinant polypeptides obtained by the expression of thehybrid nucleotide sequences are likewise part of the invention.

The invention likewise comprises the vectors characterized in that theycontain one of the hybrid nucleotide sequences. The host cellstransformed by the vectors, the transgenic organisms comprising one ofthe transformed cells as well as the procedures for preparation ofrecombinant polypeptides using the vectors, the transformed cells and/orthe transgenic organisms are, of course, likewise part of the invention.

The polypeptides according to the invention, the antibodies according tothe invention described below and the nucleotide sequences according tothe invention can advantageously be employed in procedures for thedetection and/or identification of Alicyclobacillus acidocaldarius, in asample capable of containing them. These procedures, according to thespecificity of the polypeptides, the antibodies and the nucleotidesequences according to the invention that will be used, will inparticular be able to detect and/or to identify Alicyclobacillusacidocaldarius.

The polypeptides according to the invention can advantageously beemployed in a procedure for the detection and/or the identification ofAlicyclobacillus acidocaldarius in a sample capable of containing them,characterized in that it comprises the following steps: a) contacting ofthis sample with a polypeptide or one of its fragments according to theinvention (under conditions allowing an immunological reaction betweenthe polypeptide and the antibodies possibly present in the biologicalsample); and b) demonstration of the antigen-antibody complexes possiblyformed.

Any conventional procedure can be employed for carrying out such adetection of the antigen-antibody complexes possibly formed.

By way of example, a preferred method brings into play immunoenzymaticprocesses according to the ELISA technique, by immunofluorescence, orradioimmunological processes (RIA) or their equivalent.

Thus, the invention likewise relates to the polypeptides according tothe invention, labeled with the aid of an adequate label, such as, ofthe enzymatic, fluorescent or radioactive type.

Such methods comprise, for example, the following steps: deposition ofdetermined quantities of a polypeptide composition according to theinvention in the wells of a microtiter plate, introduction into thewells of increasing dilutions of serum, or of a biological sample otherthan that defined previously, having to be analyzed, incubation of thewells of the microtiter plate, introduction into the wells of themicrotiter plate of labeled antibodies directed against pigimmunoglobulins, the labeling of these antibodies having been carriedout with the aid of an enzyme selected from those which are capable ofhydrolyzing a substrate by modifying the absorption of the radiation ofthe latter, at least at a determined wavelength, for example, at 550 nm,detection, by comparison with a control test, of the quantity ofhydrolyzed substrate.

The polypeptides according to the invention allow monoclonal orpolyclonal antibodies to be prepared which are characterized in thatthey specifically recognize the polypeptides according to the invention.It will advantageously be possible to prepare the monoclonal antibodiesfrom hybridomas according to the technique described by Kohler andMilstein in 1975. It will be possible to prepare the polyclonalantibodies, for example, by immunization of an animal, in particular amouse, with a polypeptide or a DNA, according to the invention,associated with an adjuvant of the immune response, and thenpurification of the specific antibodies contained in the serum of theimmunized animals on an affinity column on which the polypeptide, whichhas served as an antigen, has previously been immobilized. Thepolyclonal antibodies according to the invention can also be prepared bypurification, on an affinity column on which a polypeptide according tothe invention has previously been immobilized, of the antibodiescontained in the serum of an animal immunologically challenged byAlicyclobacillus acidocaldarius, or a polypeptide or fragment accordingto the invention.

The invention likewise relates to mono- or polyclonal antibodies ortheir fragments, or chimeric antibodies, characterized in that they arecapable of specifically recognizing a polypeptide according to theinvention.

It will likewise be possible for the antibodies of the invention to belabeled in the same manner as described previously for the nucleicprobes of the invention, such as a labeling of enzymatic, fluorescent orradioactive type.

The invention is additionally directed at a procedure for the detectionand/or identification of Alicyclobacillus acidocaldarius in a sample,characterized in that it comprises the following steps: a) contacting ofthe sample with a mono- or polyclonal antibody according to theinvention (under conditions allowing an immunological reaction betweenthe antibodies and the polypeptides of Alicyclobacillus acidocaldariuspossibly present in the biological sample); and b) demonstration of theantigen-antibody complex possibly formed.

The present invention likewise relates to a procedure for the detectionand/or the identification of Alicyclobacillus acidocaldarius in asample, characterized in that it employs a nucleotide sequence accordingto the invention.

More particularly, the invention relates to a procedure for thedetection and/or the identification of Alicyclobacillus acidocaldariusin a sample, characterized in that it contains the following steps: a)if need be, isolation of the DNA from the sample to be analyzed; b)specific amplification of the DNA of the sample with the aid of at leastone primer, or a pair of primers, according to the invention; and c)demonstration of the amplification products.

These can be detected, for example, by the technique of molecularhybridization utilizing a nucleic probe according to the invention. Thisprobe will advantageously be labeled with a nonradioactive (cold probe)or radioactive isotope.

For the purposes of the present invention, “DNA of the biologicalsample” or “DNA contained in the biological sample” will be understoodas meaning either the DNA present in the biological sample considered,or possibly the cDNA obtained after the action of an enzyme of reversetranscriptase type on the RNA present in the biological sample.

A further embodiment of the invention comprises a method, characterizedin that it comprises the following steps: a) contacting of a nucleotideprobe according to the invention with a biological sample, the DNAcontained in the biological sample having, if need be, previously beenmade accessible to hybridization under conditions allowing thehybridization of the nucleotide probe with the DNA of the sample; and b)demonstration of the hybrid formed between the nucleotide probe and theDNA of the biological sample.

The present invention also relates to a procedure according to theinvention, characterized in that it comprises the following steps: a)contacting of a nucleotide probe immobilized on a support according tothe invention with a biological sample, the DNA of the sample having, ifneed be, previously been made accessible to hybridization, underconditions allowing the hybridization of the nucleotide probe with theDNA of the sample; b) contacting of the hybrid formed between thenucleotide probe immobilized on a support and the DNA contained in thebiological sample, if need be after elimination of the DNA of thebiological sample which has not hybridized with the nucleotide probe,with a nucleotide probe labeled according to the invention; and c)demonstration of the novel hybrid formed in step b).

According to an advantageous embodiment of the procedure for detectionand/or identification defined previously, this is characterized in that,prior to step a), the DNA of the biological sample is first amplifiedwith the aid of at least one primer according to the invention.

Embodiments of methods include placing a recombinant, purified, and/orisolated polypeptide selected from the group consisting of a polypeptidehaving at least 90% sequence identity to SEQ ID NOS: 1, 18, 35, 52, 69,86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307,324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545,562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766, 783,800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021,1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310,1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514,1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718,1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922,1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126,2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330,2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636,2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840,2859, 2876, 2893, 2910, and 2927 in, or replacing a component, of anin-vitro transcription system such as, by way of non-limiting example, apolymerase chain reaction or a reticulocyte lysatetranscription/translation system.

Further embodiments of methods include placing a cell producing orencoding a recombinant, purified, and/or isolated nucleotide sequencecomprising a nucleotide sequence selected from the group consisting of anucleotide sequence having at least 90% sequence identity to at leastone of the sequences of SEQ ID NOS: 2, 19, 36, 53, 70, 87, 104, 121,138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359,376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597,614, 631, 648, 665, 682, 699, 716, 733, 750, 767, 784, 801, 818, 835,852, 869, 886, 903, 920, 937, 954, 971, 988, 1005, 1022, 1039, 1056,1073, 1090, 1107, 1124, 1141, 1158, 1175, 1192, 1294, 1311, 1328, 1345,1362, 1379, 1396, 1413, 1430, 1447, 1464, 1481, 1498, 1515, 1532, 1549,1566, 1583, 1600, 1617, 1634, 1651, 1668, 1685, 1702, 1719, 1736, 1753,1770, 1787, 1804, 1821, 1838, 1855, 1872, 1889, 1906, 1923, 1940, 1957,1974, 1991, 2008, 2025, 2042, 2059, 2076, 2093, 2110, 2127, 2144, 2161,2178, 2195, 2212, 2229, 2246, 2263, 2280, 2297, 2314, 2331, 2348, 2365,2382, 2399, 2416, 2518, 2535, 2552, 2569, 2603, 2620, 2637, 2654, 2671,2688, 2705, 2722, 2739, 2756, 2773, 2790, 2807, 2824, 2841, 2857, 2858,2860, 2877, 2894, 2911, and 2928 and/or a recombinant, purified, and/orisolated polypeptide selected from the group consisting of a polypeptidehaving at least 90% sequence identity to at least one of the sequencesof SEQ ID NOS: 1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205,222, 239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443,460, 477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681,698, 715, 732, 749, 766, 783, 800, 817, 834, 851, 868, 885, 902, 819,936, 953, 970, 987, 1004, 1021, 1038, 1055, 1072, 1089, 1106, 1123,1140, 1157, 1174, 1191, 1293, 1310, 1327, 1344, 1361, 1378, 1395, 1412,1429, 1446, 1463, 1480, 1497, 1514, 1531, 1548, 1565, 1582, 1599, 1616,1633, 1650, 1667, 1684, 1701, 1718, 1735, 1752, 1769, 1786, 1803, 1820,1837, 1854, 1871, 1888, 1905, 1922, 1939, 1956, 1973, 1990, 2007, 2024,2041, 2058, 2075, 2092, 2109, 2126, 2143, 2160, 2177, 2194, 2211, 2228,2245, 2262, 2279, 2296, 2313, 2330, 2347, 2364, 2381, 2398, 2415, 2517,2534, 2551, 2568, 2602, 2619, 2636, 2653, 2670, 2687, 2704, 2721, 2738,2755, 2772, 2789, 2806, 2823, 2840, 2859, 2876, 2893, 2910, and 2927 inan environment comprising temperatures at or above about 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/ora pH at, below, and/or above 8, 7, 6, 5, 4, 3, 2, 1, and/or 0.

The present invention provides cells that have been geneticallymanipulated to have an altered capacity to produce expressed proteins.In particular, the present invention relates to Gram-positivemicroorganisms, such as Bacillus species having enhanced expression of aprotein of interest, wherein one or more chromosomal genes have beeninactivated, and/or wherein one or more chromosomal genes have beendeleted from the Bacillus chromosome. In some further embodiments, oneor more indigenous chromosomal regions have been deleted from acorresponding wild-type Bacillus host chromosome. In furtherembodiments, the Bacillus is an Alicyclobacillus sp. or Alicyclobacillusacidocaldarius.

In additional embodiments, methods of modulating transcription ortranscription or transcriptional control at temperatures at or aboveabout 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95degrees Celsius and/or at a pH at, below, and/or above 8, 7, 6, 5, 4, 3,2, 1, and/or 0 via a recombinant, purified, and/or isolated nucleotidesequence comprising a nucleotide sequence selected from the groupconsisting of a nucleotide sequence having at least 90% sequenceidentity to at least one of the sequences of SEQ ID NOS: 2, 19, 36, 53,70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240, 257, 274, 291, 308,325, 342, 359, 376, 393, 410, 427, 444, 461, 478, 495, 512, 529, 546,563, 580, 597, 614, 631, 648, 665, 682, 699, 716, 733, 750, 767, 784,801, 818, 835, 852, 869, 886, 903, 920, 937, 954, 971, 988, 1005, 1022,1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158, 1175, 1192, 1294, 1311,1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447, 1464, 1481, 1498, 1515,1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651, 1668, 1685, 1702, 1719,1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855, 1872, 1889, 1906, 1923,1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059, 2076, 2093, 2110, 2127,2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263, 2280, 2297, 2314, 2331,2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552, 2569, 2603, 2620, 2637,2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773, 2790, 2807, 2824, 2841,2857, 2858, 2860, 2877, 2894, 2911, and 2928 and/or a recombinant,purified, and/or isolated polypeptide selected from the group consistingof a polypeptide having at least 90% sequence identity to at least oneof the sequences of SEQ ID NOS: 1, 18, 35, 52, 69, 86, 103, 120, 137,154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358, 375,392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596, 613,630, 647, 664, 681, 698, 715, 732, 749, 766, 783, 800, 817, 834, 851,868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021, 1038, 1055, 1072,1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310, 1327, 1344, 1361,1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514, 1531, 1548, 1565,1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718, 1735, 1752, 1769,1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922, 1939, 1956, 1973,1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126, 2143, 2160, 2177,2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330, 2347, 2364, 2381,2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636, 2653, 2670, 2687,2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840, 2859, 2876, 2893,2910, and 2927.

Further embodiments of the invention may comprise a kit for modulatingtranscription or transcriptional control, the kit comprising arecombinant, purified, and/or isolated nucleotide sequence comprising anucleotide sequence selected from the group consisting of a nucleotidesequences having at least 90% sequence identity to at least one of thesequences of SEQ ID NOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172,189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410,427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648,665, 682, 699, 716, 733, 750, 767, 784, 801, 818, 835, 852, 869, 886,903, 920, 937, 954, 971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107,1124, 1141, 1158, 1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396,1413, 1430, 1447, 1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600,1617, 1634, 1651, 1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804,1821, 1838, 1855, 1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008,2025, 2042, 2059, 2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212,2229, 2246, 2263, 2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416,2518, 2535, 2552, 2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722,2739, 2756, 2773, 2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894,2911, and 2928 and/or a recombinant, purified, and/or isolatedpolypeptide selected from the group consisting of a polypeptide havingat least 90% sequence identity to at least one of the sequences of SEQID NOS: 1, 18, 35, 52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222,239, 256, 273, 290, 307, 324, 341, 358, 375, 392, 409, 426, 443, 460,477, 494, 511, 528, 545, 562, 579, 596, 613, 630, 647, 664, 681, 698,715, 732, 749, 766, 783, 800, 817, 834, 851, 868, 885, 902, 819, 936,953, 970, 987, 1004, 1021, 1038, 1055, 1072, 1089, 1106, 1123, 1140,1157, 1174, 1191, 1293, 1310, 1327, 1344, 1361, 1378, 1395, 1412, 1429,1446, 1463, 1480, 1497, 1514, 1531, 1548, 1565, 1582, 1599, 1616, 1633,1650, 1667, 1684, 1701, 1718, 1735, 1752, 1769, 1786, 1803, 1820, 1837,1854, 1871, 1888, 1905, 1922, 1939, 1956, 1973, 1990, 2007, 2024, 2041,2058, 2075, 2092, 2109, 2126, 2143, 2160, 2177, 2194, 2211, 2228, 2245,2262, 2279, 2296, 2313, 2330, 2347, 2364, 2381, 2398, 2415, 2517, 2534,2551, 2568, 2602, 2619, 2636, 2653, 2670, 2687, 2704, 2721, 2738, 2755,2772, 2789, 2806, 2823, 2840, 2859, 2876, 2893, 2910, and 2927.

In embodiments of the invention any one of the isolated and/or purifiedpolypeptides according to the invention may be enzymatically orfunctionally active at temperatures at or above about 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and/or 95 degrees Celsius and/ormay be enzymatically or functionally active at a pH at, below, and/orabove 8, 7, 6, 5, 4, 3, 2, 1, and/or 0. In further embodiments of theinvention, glycosylation, pegylation, and/or other post-translationalmodification may be required for the isolated and/or purifiedpolypeptides according to the invention to be enzymatically orfunctionally active at a pH at or below 8, 7, 6, 5, 4, 3, 2, 1, and/or 0or at temperatures at or above about 25, 30, 35, 40, 45, 50, 55, 60, 65,70, 75, 80, 85, 90, and/or 95 degrees Celsius.

The invention is described in additional detail in the followingillustrative examples. Although the examples may represent only selectedembodiments of the invention, it should be understood that the followingexamples are illustrative and not limiting.

EXAMPLES Example 1 Transcription and Transcriptional Control UsingNucleotide and Amino Acid Sequences from Alicyclobacillus acidocaldarius

Provided in SEQ ID NOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172,189, 206, 223, 240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410,427, 444, 461, 478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648,665, 682, 699, 716, 733, 750, 767, 784, 801, 818, 835, 852, 869, 886,903, 920, 937, 954, 971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107,1124, 1141, 1158, 1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396,1413, 1430, 1447, 1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600,1617, 1634, 1651, 1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804,1821, 1838, 1855, 1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008,2025, 2042, 2059, 2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212,2229, 2246, 2263, 2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416,2518, 2535, 2552, 2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722,2739, 2756, 2773, 2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894,2911, and 2928 are a nucleotide sequences isolated from Alicyclobacillusacidocaldarius and coding for the polypeptides of SEQ ID NOS: 1, 18, 35,52, 69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290,307, 324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528,545, 562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766,783, 800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004,1021, 1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293,1310, 1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497,1514, 1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701,1718, 1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905,1922, 1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109,2126, 2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313,2330, 2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619,2636, 2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823,2840, 2859, 2876, 2893, 2910, and 2927. The nucleotide sequences of SEQID NOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223,240, 257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461,478, 495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699,716, 733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937,954, 971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141,1158, 1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430,1447, 1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634,1651, 1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838,1855, 1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042,2059, 2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246,2263, 2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535,2552, 2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756,2773, 2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and2928 are placed into expression vectors using techniques standard in theart. The vectors are then provided to cells such as bacteria cells oreukaryotic cells such as Sf9 cells or CHO cells. In conjunction with thenormal machinery in present in the cells, the vectors comprising SEQ IDNOS: 2, 19, 36, 53, 70, 87, 104, 121, 138, 155, 172, 189, 206, 223, 240,257, 274, 291, 308, 325, 342, 359, 376, 393, 410, 427, 444, 461, 478,495, 512, 529, 546, 563, 580, 597, 614, 631, 648, 665, 682, 699, 716,733, 750, 767, 784, 801, 818, 835, 852, 869, 886, 903, 920, 937, 954,971, 988, 1005, 1022, 1039, 1056, 1073, 1090, 1107, 1124, 1141, 1158,1175, 1192, 1294, 1311, 1328, 1345, 1362, 1379, 1396, 1413, 1430, 1447,1464, 1481, 1498, 1515, 1532, 1549, 1566, 1583, 1600, 1617, 1634, 1651,1668, 1685, 1702, 1719, 1736, 1753, 1770, 1787, 1804, 1821, 1838, 1855,1872, 1889, 1906, 1923, 1940, 1957, 1974, 1991, 2008, 2025, 2042, 2059,2076, 2093, 2110, 2127, 2144, 2161, 2178, 2195, 2212, 2229, 2246, 2263,2280, 2297, 2314, 2331, 2348, 2365, 2382, 2399, 2416, 2518, 2535, 2552,2569, 2603, 2620, 2637, 2654, 2671, 2688, 2705, 2722, 2739, 2756, 2773,2790, 2807, 2824, 2841, 2857, 2858, 2860, 2877, 2894, 2911, and 2928produce the polypeptides of SEQ ID NOS: 1, 18, 35, 52, 69, 86, 103, 120,137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307, 324, 341, 358,375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545, 562, 579, 596,613, 630, 647, 664, 681, 698, 715, 732, 749, 766, 783, 800, 817, 834,851, 868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021, 1038, 1055,1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310, 1327, 1344,1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514, 1531, 1548,1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718, 1735, 1752,1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922, 1939, 1956,1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126, 2143, 2160,2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330, 2347, 2364,2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636, 2653, 2670,2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840, 2859, 2876,2893, 2910, and 2927. The polypeptides of SEQ ID NOS: 1, 18, 35, 52, 69,86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307,324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545,562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766, 783,800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021,1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310,1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514,1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718,1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922,1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126,2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330,2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636,2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840,2859, 2876, 2893, 2910, and 2927 are then isolated and/or purified. Theisolated and/or purified polypeptides of SEQ ID NOS: 1, 18, 35, 52, 69,86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307,324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545,562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766, 783,800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021,1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310,1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514,1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718,1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922,1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126,2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330,2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636,2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840,2859, 2876, 2893, 2910, and 2927 are then each demonstrated to have oneor more of the activities provided in Table 1.

The isolated and/or purified polypeptides of SEQ ID NOS: 1, 18, 35, 52,69, 86, 103, 120, 137, 154, 171, 188, 205, 222, 239, 256, 273, 290, 307,324, 341, 358, 375, 392, 409, 426, 443, 460, 477, 494, 511, 528, 545,562, 579, 596, 613, 630, 647, 664, 681, 698, 715, 732, 749, 766, 783,800, 817, 834, 851, 868, 885, 902, 819, 936, 953, 970, 987, 1004, 1021,1038, 1055, 1072, 1089, 1106, 1123, 1140, 1157, 1174, 1191, 1293, 1310,1327, 1344, 1361, 1378, 1395, 1412, 1429, 1446, 1463, 1480, 1497, 1514,1531, 1548, 1565, 1582, 1599, 1616, 1633, 1650, 1667, 1684, 1701, 1718,1735, 1752, 1769, 1786, 1803, 1820, 1837, 1854, 1871, 1888, 1905, 1922,1939, 1956, 1973, 1990, 2007, 2024, 2041, 2058, 2075, 2092, 2109, 2126,2143, 2160, 2177, 2194, 2211, 2228, 2245, 2262, 2279, 2296, 2313, 2330,2347, 2364, 2381, 2398, 2415, 2517, 2534, 2551, 2568, 2602, 2619, 2636,2653, 2670, 2687, 2704, 2721, 2738, 2755, 2772, 2789, 2806, 2823, 2840,2859, 2876, 2893, 2910, and 2927 are placed in an extracellulartranscription system and are demonstrated to have activity intranscription or modulating transcription.

Example 2 Transcriptional Control Using Catabolite-Responsive Elementsfrom Alicyclobacillus acidocaldarius

Provided in SEQ ID NOS: 2857, 2858, 2860, 2877, 2894, 2911, and 2928 arenucleotide sequences isolated from Alicyclobacillus acidocaldarius. Thenucleotide sequences of SEQ ID NOS: 2857, 2858, 2860, 2877, 2894, 2911,and 2928 are placed into expression vectors and functionally linked to areporter gene using techniques standard in the art. The vectors are thenprovided to cells such as bacteria cells or eukaryotic cells such as Sf9cells or CHO cells. In conjunction with the normal machinery in presentin the cells, the vectors comprising SEQ ID NOS: 2857, 2858, 2860, 2877,2894, 2911, and 2928 attempt to produce the protein coded for by thereporter gene in an environment designed to assay the function of acatabolite-responsive element. The cells are then assayed for thepresence or absence and/or level of the reporter gene product. SEQ IDNOS: 2857, 2858, 2860, 2877, 2894, 2911, and 2928 are then eachdemonstrated to have activity as a catabolite-responsive element.

All references, including publications, patents, and patentapplications, cited herein are hereby incorporated by reference to thesame extent as if each reference were individually and specificallyindicated to be incorporated by reference and were set forth in itsentirety herein.

While this invention has been described in certain embodiments, thepresent invention can be further modified within the spirit and scope ofthis disclosure. This application is therefore intended to cover anyvariations, uses, or adaptations of the invention using its generalprinciples. Further, this application is intended to cover suchdepartures from the present disclosure as come within known or customarypractice in the art to which this invention pertains and that fallwithin the limits of the appended claims and their legal equivalents.

BIBLIOGRAPHIC REFERENCES

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What is claimed is:
 1. An expression vector comprising a nucleic acidencoding a polypeptide having at least 95% sequence identity to SEQ IDNO: 1497 and wherein the polypeptide is a central glycolytic genesregulator.
 2. The expression vector of claim 1, wherein the polypeptideis a central glycolytic genes regulator at a temperature at or above 50degrees Celsius.
 3. The expression vector isolated of claim 1, whereinthe polypeptide has 100% identity to SEQ ID NO:
 1497. 4. The expressionvector isolated of claim 1, wherein the nucleic acid has at least 95%identity to SEQ ID NO:
 1498. 5. The expression vector isolated of claim1, wherein the nucleic acid has 100% identity to SEQ ID NO:
 1498. 6. Acell comprising the expression vector of claim
 1. 7. A method ofmodulating transcription or transcriptional control at temperatures ator above 25 degrees Celsius, the method comprising providing to atranscriptional system the expression vector of claim
 1. 8. The methodaccording to claim 7, wherein providing to a transcriptional system theexpression vector of claim 1 occurs at a temperature at or above 50degrees Celsius.